US20210388442A1 - Method and devices for age determination - Google Patents

Method and devices for age determination Download PDF

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US20210388442A1
US20210388442A1 US17/283,775 US201917283775A US2021388442A1 US 20210388442 A1 US20210388442 A1 US 20210388442A1 US 201917283775 A US201917283775 A US 201917283775A US 2021388442 A1 US2021388442 A1 US 2021388442A1
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age
genomic dna
dna sequences
individual
methylation
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Tim Schiederig
Sheraz Gul
Andrea Zaliani
Laura Chachulski
Carsten Claussen
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Thomas Jc Matzen GmbH
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

Definitions

  • the present invention relates to the determination of ages. Specifically, the present invention relates to a method for determining an age indicator, and a method for determining the age of an individual. Said methods are based on data comprising the DNA methylation levels of a set of genomic DNA sequences. Preferably, said age indicator is determined by applying on the data a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), preferably in combination with subsequent stepwise regression. Furthermore, the invention relates to an ensemble of genomic DNA sequences and a gene set, and their uses for diagnosing the health state and/or the fitness state of an individual and identifying a molecule which affects ageing. In further aspects, the invention relates to a chip or a kit, in particular which can be used for detecting the DNA methylation levels of said ensemble of genomic DNA sequences.
  • LASSO Least Absolute Shrinkage and Selection Operator
  • the chronological age is not the ideal indicator for the age-associated health state of an individual which is often called the “biological age”. Determination of an age which is more similar to the biological age might be helpful in assessing whether or not an individual has a higher risk for ageing-related diseases such as Alzheimer's disease. If the determined age is higher than the chronological age, preventive measures, e.g. a change in life-style, might be indicated to prevent or slow down the course of ageing-related diseases. The determination of an alternative age might be also useful for improving diagnostics, for example, evaluating, if a focus should be put on ageing-related diseases or not.
  • the alternative age when used as an indicator of the chronological age. If the alternative age determination is based on a biological sample, it may be used, for example, also in forensics, where traces of blood from an offender are found at a crime scene.
  • CpG loci about 28 Million CpG loci can be found in the human genome. Even if it is considered that methylation levels of some of these CpG loci might not be affected by aging, a very large number of CpG loci remain that have methylation levels affected by age. While it is believed that the detection methods used in determining methylation levels might improve over time, allowing to determine the methylation levels of a growing number of CpG loci, it is currently possible already to determine the methylation levels of at least app. 800.000 (800000) CpG loci using commercially available instruments and methods. Still, such measurements are expensive, and thus, the determination of an age based on measuring a very large number of CpG loci would be very expensive.
  • the present invention relates to a method for determining an age indicator, a method for determining the age of an individual, and/or an ensemble of genomic DNA sequences.
  • the method for determining an age indicator of the invention comprises the steps of
  • the method for determining the age of an individual comprises the steps of
  • the ensemble of genomic DNA sequences comprises least one, preferably at least 10, preferably at least 50, preferably at least 70, preferably all of cg11330075, cg25845463, cg22519947, cg21807065, cg09001642, cg18815943, cg06335143, cg01636910, cg10501210, cg03324695, cg19432688, cg22540792, cg11176990, cg00097800, cg27320127, cg09805798, cg03526652, cg09460489, cg18737844, cg07802350, cg10522765, cg12548216, cg00876345, cg15761531, cg05990274, cg05972734, cg03680898, cg16593468, cg19301963, cgg
  • said ensemble of genomic DNA sequences is comprised in the reduced training data set and/or the age indicator obtained by said method for determining an age indicator.
  • the invention relates to a gene set comprising at least one, preferably at least 10, preferably at least 30, preferably at least 50, preferably at least 70, preferably all of SIM bHLH transcription factor 1 (SIM1), microtubule associated protein 4 (MAP4), protein kinase C zeta (PRKCZ), glutamate ionotropic receptor AMPA type subunit 4 (GRIA4), BCL10, immune signaling adaptor (BCL10), 5′-nucleotidase domain containing 1 (NT5DC1), suppression of tumorigenicity 7 (ST7), protein kinase C eta (PRKCH), glial cell derived neurotrophic factor (GDNF), muskelin 1 (MKLN1), exocyst complex component 6B (EXOC6B), protein S (PROS1), calcium voltage-gated channel subunit alpha1 D (CACNA1D), kelch like family member 42 (KLHL42), OTU de
  • said gene set is obtained by selecting from said ensemble of genomic DNA sequences those genomic DNA sequences which encode a protein, or a microRNA or long noncoding RNA.
  • the invention relates to the use of the ensemble of genomic DNA sequences or the gene set according to the invention for diagnosing the health state and/or the fitness state of an individual.
  • the invention relates to an in silico and/or in vitro screening method for identifying a molecule which affects ageing comprising a step of providing the ensemble of genomic DNA sequences or the gene set according to the invention, wherein the molecule ameliorates, prevents and/or reverses at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer when administered to an individual.
  • the invention relates to a chip or a kit, in particular which can be used for detecting the DNA methylation levels of the ensemble of genomic DNA sequences or the gene set according to the invention.
  • the chip comprises the genomic DNA sequences or the gene set according to the invention, wherein each sequence is contained in a separate spot.
  • the kit comprises
  • the invention is, at least partly, based on the surprising discovery that an age indicator comprising a further reduced set of genomic DNA sequences, but still having an acceptable quality, could be determined by applying a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), wherein the independent variables are the methylation levels of the genomic DNA sequences and the dependent variable is the age.
  • LASSO Least Absolute Shrinkage and Selection Operator
  • Reducing the number of genomic DNA sequences while ensuring accurate age determination has many advantages.
  • One advantage is reducing costs, efforts and/or necessary expertise for determining the DNA methylation levels of the genomic DNA sequences, in particular because it allows to use simpler laboratory methods.
  • Another advantage is to narrow down drug target candidates which are encoded by the reduced ensemble of genomic DNA sequences.
  • a further advantage is to provide an alternative or improved tool for diagnosing the health state of an individual.
  • a method for determining alternative or improved age indicators is also useful for validating the results obtained by other methods, i.e. a diagnosis or drug candidates.
  • an element means one element or more than one element.
  • an age indicator refers to a statistical model which can be used for determining the age of an individual based on the DNA methylation levels of certain genomic DNA sequences of said individual.
  • the determined age of an individual is not necessarily the same age as the chronological age of said individual. Usually, the determined age and the chronological age of an individual are different, and it is coincidence when they are the same. The determined age is also termed “alternative age” herein. Any age may be counted in “years” and/or, preferably, in “days”.
  • the determined age of an individual is a better indicator of the biological age of said individual than his chronological age.
  • the chronological age of an individual refers to the time which has passed since birth of the individual.
  • the biological age as used herein, relates to the health state of an individual.
  • the health state relates to the state of at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer, wherein the state indicates the absence, presence, or stage of the disease or the phenotype associated with a disease.
  • the age indicator of the invention can be used for diagnosing the health state of an individual.
  • the age indicator refers to a linear model which comprises independent variables.
  • an independent variable comprised in the age indicator or a linear model used for generating the age indicator refers to the DNA methylation level of a certain genomic DNA sequence.
  • the dependent variable of the age indicator of the invention and/or the linear model used for generating the age indicator of the invention is the age.
  • the age of a plurality of individuals is predicted by a set of independent variables (the methylation levels of certain genomic DNA sequences), wherein each independent variable has at least one coefficient.
  • the predicted age and the chronological age preferably correlate very well or, in other words, are preferably in average very similar.
  • the predicted age also termed herein the “determined age”, of one individual, may differ, for example for several years, from his chronological age.
  • the methylation level refers to the beta value.
  • the beta value describes the ratio of methylated cytosines over the sum of methylated and unmethylated cytosines among all relevant cytosines within a certain part of the genomic DNA of all alleles of all cells contained in a sample.
  • the methylation state of one particular cytosine molecule is binary and is either unmethylated (0; 0%) or methylated (1; 100%).
  • a methylated cytosine is also termed “5′mC”.
  • the beta value for a cytosine at a particular position in the genomic DNA of a single cell having two alleles is thus usually either 0, 0.5 or 1.
  • the beta value at a particular CpG position in the genomic DNA of a population of cells can take a value between 0 and 1.
  • the beta value when considering all CpGs within a certain genomic DNA sequence of a single allele can take a value between 0 and 1.
  • only one CpG is considered within a certain genomic DNA sequence.
  • the sample comprises preferably more than one cell which might comprise more than one allele.
  • the beta value of a genomic DNA sequence can virtually take any value between 0 and 1.
  • the methylation level of a CpG is defined by the cytosine, and not the guanine, comprised in said CpG.
  • CGs/CpGs correspond to IlluminaTM probes specified by so called Cluster CG numbers (IlluminaTM methylation probe ID numbers).
  • the methylation levels of a preselected set of CpGs can be measured using an IlluminaTM DNA methylation array.
  • an IlluminaTM methylation probe ID is characterized by the term “cg” followed by a number, for example cg11330075 or cg25845463.
  • the terms “CG”, “cg”, “CpG”, “CpG locus”, “CpG site”, and “cg site” are used interchangeably herein.
  • methylation levels of CpGs can be quantified using other methods known in the art as well. Nonetheless, unless indicated otherwise, the CGs/CpGs identified in the present invention correspond to the IlluminaTM methylation probe IDs.
  • methylation level of a genomic DNA sequence it is not required for determining the methylation level of a genomic DNA sequence to determine the methylation of cytosines at a single-nucleotide resolution, but the average methylation signal of relevant cytosines within said sequence is sufficient.
  • cytosines which are followed by a guanine CpG dinucleotides
  • the common names for bases and nucleotides, e.g. cytosine and cytidine, respectively, are used interchangeably herein and refer to a specific nucleotide comprising the respective base.
  • methylation level and “DNA methylation level” are used interchangeably. The ranges of 0% to 100% and 0 to 1 are used interchangeably herein when referring to methylation levels.
  • genomic DNA sequence refers to a coherent part of the genomic DNA of an individual.
  • a certain genomic DNA sequence does not have to be necessarily identical to the reference sequence of the genomic DNA sequence it relates to, but it may be a variant thereof.
  • the genomic DNA sequence is a unique sequence.
  • a skilled person can easily determine if a sequence is a variant of a certain reference genomic DNA sequence by interrogating databases such as “GenBank” or “EMBL-NAR” and using general knowledge.
  • the methylation level of a genomic DNA sequence refers to the methylation level of at least one cytosine within at least one CpG dinucleotide comprised in said genomic DNA sequence.
  • the methylation level of a genomic DNA sequence refers to the methylation level of exactly one cytosine within exactly one CpG dinucleotide comprised in said genomic DNA sequence.
  • said genomic DNA sequence comprises further nucleotides whereof the methylation levels are not considered, but which allow identification of said CpG dinucleotide.
  • a genomic DNA sequence may be defined by a CpG locus.
  • a genomic DNA sequence is defined by an IlluminaTM methylation probe ID.
  • a plurality of individuals refers to more than one individual.
  • An individual refers to a living being which has 5′-methylated cytosines (5′-mc) within its genomic DNA.
  • a living being is a vertebrate, more preferably a mammal, most preferably a human.
  • the methylation level of at least one genomic DNA sequence of the individual is associable with ageing and/or the health state of the individual.
  • an individual can have any sex, for example, it may be a male, a female, a hermaphrodite or others.
  • the terms “he”, “she”, “it”, or “his”, “her”, “its” are used interchangeably herein in the context of an individual.
  • the identity of an individual is known, but this is not required.
  • the age of an individual can be determined by the method of the invention even if the identity and/or the chronological age of the individual is unknown.
  • the method for determining the age of an individual according to the present invention allows to predict the chronological age of an individual whereof only a biological sample is available.
  • a biological sample comprises, for example, hair cells, buccal cells, saliva, blood and/or sperm.
  • the method for determining the age of an individual is useful for estimating the chronological age of an individual who was present at a crime scene and has left some of his/her biological material there.
  • the method for determining the age of an individual is useful for estimating the chronological age of an individual when no data about the chronological age of said individual have been recorded or are available.
  • a regression method refers to a statistical process for estimating the relationships among variables, in particular the relationship between a dependent variable and one or more independent variables. Regression analysis is also used to understand which among the independent variables are related to the dependent variable, and to explore the forms of these relationships.
  • the regression method comprises a linear regression.
  • the regression method comprises a linear regression that uses shrinkage. Shrinkage is where data values are shrunk towards a central point, like the mean.
  • the regression method comprises a Least Absolute Shrinkage and Selection Operator (LASSO).
  • LASSO encourages simple, sparse models (i.e. models with fewer parameters). This particular type of regression is well-suited for models showing high levels of multicollinearity or when automation of certain parts of the model selection is desired, like variable selection and/or parameter elimination.
  • LASSO regression performs L1 regularization, which adds a penalty equal to the absolute value of the magnitude of coefficients. This type of regularization can result in sparse models with few coefficients; some coefficients can become zero and eliminated from the model. Larger penalties result in coefficient values closer to zero, which is the ideal for producing simpler models. In other words, LASSO can be used for reducing the number of independent variables of a linear model.
  • the terms “LASSO”, “lasso” and “Lasso regression” are used synonymously herein.
  • the LASSO is performed with the biglasso R package, preferably by applying the command “cv.biglasso”.
  • the “nfold” is 20.
  • the LASSO L1 regularization parameter/alpha parameter is 1.
  • the regression method of the invention does not comprise a Ridge regression (L2 regularization) or the L2 regularization parameter/lambda parameter is 0.
  • the L1 regularization parameter or alpha parameter is not 1, but around 0.1 to 0.9.
  • the Elastic Net method comprises a Ridge regression.
  • the regression method of the invention does not comprise an Elastic Net method.
  • the age indicator of the invention is preferably not determined by applying an Elastic Net method.
  • the regression method of the invention further comprises applying a stepwise regression subsequently to the LASSO.
  • the stepwise regression is applied on the reduced training data set.
  • the method for determining an age indicator comprises the steps of
  • the method for determining the age of an individual comprises the steps of
  • Stepwise regression is a method of fitting regression models in which the choice of predictive variables is carried out by an automatic procedure.
  • a variable is considered for addition to or subtraction from the set of explanatory variables based on some prespecified criterion. This may take the form of a sequence of F-tests or t-tests, but other techniques are possible, such as adjusted R2, Akaike information criterion (AIC), Bayesian information criterion, Mallows's Cp, PRESS, or false discovery rate.
  • the main approaches are forward selection, backward elimination and bidirectional elimination. Forward selection involves testing the addition of each variable using a chosen model fit criterion, adding the variable (if any) whose inclusion gives the most statistically significant improvement of the fit, and repeating this process until none improves the model to a statistically significant extent.
  • Backward elimination involves testing the deletion of each variable using a chosen model fit criterion, deleting the variable (if any) whose loss gives the most statistically insignificant deterioration of the model fit, and repeating this process until no further variables can be deleted without a statistically significant loss of fit.
  • Bidirectional elimination is a combination of forward selection and backward elimination, testing at each step for variables to be included or excluded.
  • the variables considered by the stepwise regression are the variables which are selected by the LASSO regression.
  • the stepwise regression is a bidirectional elimination.
  • statistically insignificant independent variables are removed when applying said stepwise regression.
  • significance level for determining if a variable is added/included or removed/excluded is 0.05.
  • a set of genomic DNA sequences is reduced by the regression method according to the invention in at least one step, preferably in two steps.
  • the starting set of genomic DNA sequences is preselected from genomic DNA sequences whereof the methylation level is associable with chronological age.
  • Such a preselected set is, for example, an IlluminaTM DNA methylation array.
  • the LASSO is applied thereby determining an age indicator and a reduced training data set, which both comprise an ensemble of genomic DNA sequences.
  • the set of genomic DNA sequences comprised in the training data set is preselected from genomic DNA sequences whereof the methylation level is associable with chronological age.
  • the preselected set comprises at least 400000, preferably at least 800000 genomic DNA sequences. Particularly suitable are sequences assayed by the Infinium MethylationEPIC BeadChip Kit.
  • the genomic DNA sequences comprised in the training data set are not overlapping with each other and/or only occur once per allele. This is particularly preferred, when only a comparably small set of genomic DNA sequence is preselected, i.e. less than 10000.
  • the stepwise regression is applied on the reduced training data set, thereby determining an age indicator comprising an ensemble of genomic DNA sequences.
  • the ensemble of genomic DNA sequences determined by applying LASSO and subsequent stepwise regression is smaller and the respective age indicator has a better performance than the ensemble of genomic DNA sequences or the age indicator determined by applying only LASSO without stepwise regression.
  • an age indicator determined by applying LASSO and subsequent stepwise regression had an accuracy which was at least about as high or even improved compared to prior art methods such as in Horvath, Genome Biology 2013, 14:R115.
  • the subset comprised in the age indicator is also termed “ensemble” or “ensemble of genomic DNA sequences”.
  • the subset of genomic DNA sequences (ensemble) is maximally as big as the set of genomic DNA sequences.
  • the ensemble comprised in the age indicator of the invention is smaller than the set of genomic DNA sequences used for determining said age indicator.
  • the ensemble comprised in the age indicator of the invention is smaller than the set of genomic DNA sequences comprised in the reduced training data set used for determining said age indicator.
  • the reduced training data set comprises at least 90, preferably at least 100, preferably at least 140 genomic DNA sequences.
  • the reduced training data set comprises less than 5000, preferably less than 2000, preferably less than 500, preferably less than 350, preferably less than 300 genomic DNA sequences.
  • the set of genomic DNA sequences comprised in the reduced training data set is preferably much reduced compared to the preselected set of genomic DNA sequences, preferably more than 90%, preferably more than 99%, preferably more than 99.9%.
  • said set of genomic DNA sequences must be large enough to not prematurely limit the optimization potential of subsequent stepwise regression and/or to not obtain an age indicator with a weak performance.
  • an age indicator comprising less than 30 genomic DNA sequences has a rather weak performance compared to an age indicator comprising at least 30, preferably at least 50, preferably at least 60, preferably at least 80 genomic DNA sequences.
  • an age indicator comprising as few genomic DNA sequences as possible is preferred.
  • the age indicator comprises at least 30, preferably at least 50, preferably at least 60, preferably at least 80 genomic DNA sequences.
  • the age indicator comprises less than 300, preferably less than 150, preferably less than 110, preferably less than 100, preferably less than 90 genomic DNA sequences.
  • the age indicator comprises 80 to 100, preferably 80 to 90, preferably 88 genomic DNA sequences.
  • the age indicator of the invention comprises at least one coefficient per genomic DNA sequence contained in the ensemble. Since one coefficient is sufficient, the age indicator preferably comprises exactly one coefficient per genomic DNA sequence contained in the ensemble.
  • a coefficient refers to the weight of an independent variable, which herein is the methylation level of a certain genomic DNA sequence.
  • the coefficient is multiplied with the methylation level of the genomic DNA sequence or, in other words, a weight is put on each genomic DNA sequence and its methylation level; and then all weighted methylation levels are summed up.
  • the methylation level is between 0 and 1 (unmethylated and fully methylated, respectively).
  • a reduced training data set refers to a training data set whereof the data of certain genomic DNA sequences are eliminated or not considered.
  • a reduced training data set is determined by applying a regression method comprising LASSO on a training data set.
  • the training data set comprises a matrix comprising as columns the methylation levels of the genomic DNA sequences comprised in the set of genomic DNA sequences and as rows the plurality of individuals.
  • the chronological age of said individuals is comprised in a further column of the matrix.
  • the age indicator of the invention is iteratively updated comprising adding the data of at least one further individual to the training data in each iteration, thereby iteratively expanding the training data set.
  • said iterative updating of the age indicator iteratively improves the performance of the age indicator, in particular its accuracy.
  • iterative updating refers to consecutive rounds of updating the age indicator.
  • one round of updating or updating round is specified in certain or preferred embodiments of the invention.
  • different rounds of updating may refer to the same or different embodiments.
  • each updating round of the iteration is specified by the same embodiments of the invention.
  • a further individual with regard to updating the age indicator, refers to an individual which has not contributed data to the training data set, but his data are added in an updating round.
  • Expanding the training data set refers to adding the data of at least one further individual to the training data set.
  • the added data of each further individual comprise the individual's DNA methylation levels of
  • Said option (i) refers in particular to the starting set of genomic DNA sequences, in particular to the preselected set of genomic DNA sequences.
  • this starting set of genomic DNA sequences is large and comprises, for example, at least 800000 genomic DNA sequences.
  • adding the methylation levels of at least 5% of the starting set to the training data set provides a sufficiently large training data set which can be used for determining an age indicator.
  • the training data set is restricted to the genomic DNA sequences whereof the DNA methylation levels of all individuals comprised therein are present.
  • updating the age indicator according to said option (i) comprises adding at least 50%, preferably 100% of the set of genomic DNA sequences comprised in the initial or any of the expanded training data sets, in particular if several or many updating rounds are done.
  • the set of genomic DNA sequences whereof the methylation levels are added is identical for each of the further individual(s). This is particularly useful to avoid excessive removal of genomic DNA sequences within one round of updating.
  • updating of the age indicator can change the ensemble of genomic DNA sequences (independent variables) comprised therein and/or the coefficient(s) of each said genomic DNA sequence.
  • said option (i) allows to extend, restrict and/or alter said ensemble of genomic DNA sequences, whereas option (ii) only allows to restrict said ensemble of genomic DNA sequences.
  • options (i) and (ii) allow said coefficients to change.
  • An advantage of option (ii) however is, that only the methylation levels of a reduced set of genomic DNA sequences of the at least one further individual must be provided.
  • said option (ii) is particularly useful for further reducing the size of said ensemble of genomic DNA sequences.
  • option (i) is particularly useful for generating different age indicators for different purposes, for example, age indicators for certain groups of individuals, or to determine different age indicators as a basis for further refinements; option (ii) is particularly useful for fine-tuning and optimizing a generally already useful age indicator, i.e. for further reducing the number of independent variables, for example for its non-personalized off-the-shelf use.
  • options (i) and (ii) can be combined to combine the flexibility of option (i), and the streamlining of option (ii).
  • one updating round comprises applying the LASSO on the expanded training data set, thereby determining an updated age indicator and/or an updated reduced training data set.
  • the training data set to which the data of the at least one further individual are added is the reduced training data set, which can be the initial or any of the updated reduced training data sets.
  • the reduced training data set is the previous reduced training data set in the iteration.
  • an updated reduced training data set can result from applying the LASSO on an expanded training data set and/or from adding data of at least one further individual to a reduced training data set.
  • one updating round comprises applying the stepwise regression on the reduced training data set thereby determining an updated age indicator.
  • the data of at least one individual is removed from the training data set and/or the reduced training data set.
  • the training data set, reduced training data set and/or added data further comprise at least one factor relating to a life-style or risk pattern associable with the individual(s) and/or a characteristic of the individual(s).
  • the factor is selected from drug consumption, environmental pollutants, shift work and stress.
  • the preselection of genomic DNA sequences, and/or the addition and/or removal of the data of an individual depends on at least one characteristic of the individual.
  • the characteristic of an individual is for example, the ethnos, the sex, the chronological age, the domicile, the birth place, at least one disease and/or at least one life style factor.
  • a life style factor is selected from drug consumption, exposure to an environmental pollutant, shift work or stress.
  • the training data set and/or the reduced training data set is restricted to genomic DNA sequences whereof the DNA methylation level and/or the activity/level of an encoded protein is associated with at least one of said characteristics and/or life-style factors.
  • Selecting the data in the training data set and/or the reduced training data set at any step, i.e. at the start during preselecting genomic DNA sequences and/or during updating said data sets and/or the age indicator, based on life-style factors and/or characteristics of the individuals, allows to determine age indicators which are particularly well suited for determining the age of an individual or a certain group of individuals having a certain combination of said characteristics and/or life-style factors.
  • the application of different age indicators for age determination may be useful for determining certain predispositions of an individual or a group of individuals, for example, a predominant effect of stress or drug consumption.
  • the determined age of an individual is much higher than expected when using an age indicator which has been optimized for smoking-related ageing than when using an age indicator which has been optimized for shift work related ageing, this may indicate that smoking is a more important factor for the ageing related health state of the individual than the shift work.
  • the quality of the age indicator is determined, wherein the determination of said quality comprises the steps of
  • a test data set is a data set which can be used for evaluating an age indicator that has been determined based on a training data set.
  • said training data set and test data set have the same structure.
  • the test data set and the training data set comprise the same set of genomic DNA sequences.
  • the test data set only contains data of individuals who have not contributed data to the respective training data set.
  • Evaluation of an age indicator comprises statistical evaluation and/or evaluation of the domain boundaries.
  • the age of the individuals of the test data set is determined and compared to the chronological age of said individuals. Any statistical measurement or parameter which is commonly used to describe the correlation of two variables can be applied.
  • the statistical parameter is selected from a coefficient of determination (R 2 ) and a mean absolute error (MAE).
  • R 2 coefficient of determination
  • MAE mean absolute error
  • a R 2 of greater than 0.50, preferably greater than 0.70, preferably greater than 0.90, preferably greater than 0.98 and/or a MAE of less than 6 years, preferably less than 4 years, preferably at most 1 year indicates an acceptable quality. If not specified herein, a skilled person can evaluate the result of the measurement or the parameter based on common knowledge. In case of doubt, the quality should be judged as not acceptable.
  • the domain boundaries of an age indicator refer to the minimum and maximum DNA methylation levels of each genomic DNA sequence comprised in the age indicator. More specifically, said minimum and maximum DNA methylation levels are found in the training data set which has been used for determining the age indicator.
  • the test data set should have a reasonable size. In particular for the statistical evaluation, it should not be too small, but comprise at least 10, preferably at least 30 individuals, preferably at least 200 individuals. For determination of the domain boundaries, the test data set should additionally not be too large, and thus comprise at most 1000 individuals, preferably at most 200 individuals. If it is larger, some violations of the domain boundaries may be allowable, for example for 5%, preferably for 1% of the individuals of the test data set.
  • the training data set and/or the test data set comprises at least 10, preferably at least 30 individuals, preferably at least 200 individuals.
  • the training data set comprises at least 200 individuals and the test data set comprises at least 30 individuals.
  • an age indicator which has been judged to not have an acceptable quality can still be useful for the determination of the age on an individual.
  • accepted quality refers to the determination of an optimal age indicator, in particular through updating.
  • an acceptable or unacceptable quality of an age indicator does not relate to the absolute quality of the age indicator, but to its relative quality compared to other age indicators, in particular to age indicators determined in different rounds of updating according to the method of the invention.
  • the age indicator is updated when its quality is not acceptable.
  • the quality is judged to be acceptable or not acceptable as explained above in the context of evaluation of the age indicator.
  • the age indicator is not further updated when the number of individuals comprised in the data has reached a predetermined value and/or a predetermined time has elapsed since a previous update.
  • the predetermined time may also refer to the number of quality evaluations for potential updating rounds.
  • an age indicator comprises already data of many thousands or even millions of individuals, or the last 10 or even 100 evaluations with new test data sets have indicated an acceptable quality, further optimization of the age indicator is not to be expected and the updating may stop.
  • the DNA methylation levels of the genomic DNA sequences of an individual are measured in a sample of biological material of said individual comprising said genomic DNA sequences.
  • the sample comprises buccal cells.
  • Suitable methods for determining DNA methylation levels are, for example, methylation sequencing, bisulfate sequencing, a PCR method, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), methylation-sensitive single-strand conformation analysis, methyl-sensitive cut counting (MSCC), base-specific cleavage/MALDI-TOF, combined bisulfate restriction analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), micro array-based methods, bead array-based methods, pyrosequencing and/or direct sequencing without bisulfate treatment (nanopore technology).
  • HRM high resolution melting analysis
  • MS-SnuPE methylation-sensitive single-nucleotide primer extension
  • MSCC methyl-sensitive single-strand conformation analysis
  • MSCC methyl-sensitive cut counting
  • COBRA combined bisulfate restriction analysis
  • MeDIP methylated DNA immunoprecipitation
  • micro array-based methods bea
  • the DNA methylation levels of an individual are measured with a DNA methylation array such as an IlluminaTM DNA methylation array, preferably an Infinium MethylationEPIC BeadChip Kit.
  • a DNA methylation array is particularly suitable when the DNA methylation levels of a very large number of genomic DNA sequences are to be measured, in particular for starting and/or preselected genomic DNA sequences.
  • the DNA methylation levels of genomic DNA sequences of an individual are measured by base-specific cleavage/MALDI-TOF and/or a PCR method, preferably wherein base-specific cleavage/MALDI-TOF is the Agena technology and the PCR method is methylation specific PCR.
  • Base-specific cleavage/MALDI-TOF and/or a PCR method is particularly suitable when DNA methylation levels of a reduced set of genomic DNA sequences is to be measured, in particular for adding data to the reduced training data set and/or providing the methylation levels of an individual for whom the age is to be determined with the age indicator of the invention.
  • the method for determining an age indicator and/or the method for determining the age of an individual according to the present invention further comprise a step of obtaining a sample of biological material of an individual.
  • the biological material may be derived from any part of the individual, but preferably the sample is obtained noninvasively.
  • the individual is not an embryo.
  • the sample is obtained from a buccal swab.
  • the age indicator of the invention can be used as a tool for determining the age of an individual.
  • the method for determining the age of an individual according to the invention comprises all steps of the method of the invention for determining an age indicator or comprises a step of providing an age indicator according to the invention.
  • said method of determining the age of an individual comprises the steps of providing the DNA methylation levels of the individual for whom the age is to be determined of at least 80%, preferably 100% of the genomic DNA sequences comprised in said age indicator and determining the age of the individual based on its DNA methylation levels and said age indicator.
  • the methylation levels of at least 80%, preferably 100%, of the genomic DNA sequences comprised in the provided age indicator must be provided for an individual for whom the age is to be determined.
  • the methylation levels of the genomic DNA sequences of said individual which are missing can be imputed, for example by using the median or mean of the provided methylation levels.
  • the age of the individual is determined based on its DNA methylation levels and the updated age indicator. In particular, the age is determined on the updated age indicator when the quality of the initially provided age indicator is not acceptable.
  • the age of the individual is only determined with the age indicator when he/she has not contributed data to the training data set which is or has been used for generating said age indicator.
  • the method for determining the age of an individual further comprises a step of determining at least one life-style factor which is associated with the difference between the determined and the chronological age of said individual.
  • the ensemble of genomic DNA sequences according to the invention does not comprise cg27320127.
  • the ensemble of genomic DNA sequences according to the invention comprises at least one, preferably at least 4, preferably at least 10, preferably at least 30, preferably at least 70, preferably all of cg11330075, cg00831672, cg27320127, cg27173374, cg14681176, cg06161948, cg08224787, cg05396610, cg15609017, cg09805798, cg19215678, cg12333719, cg03741619, cg16677512, cg03230469, cg19851481, cg10543136, cg07291317, cg26430984, cg16950671, cg16867657, cg22077936, cg08044253, cg12548216, cg05211227, cg13759931, cg08686931, cg0795
  • said ensemble of genomic DNA sequences is comprised in the age indicator obtained by the method for determining an age indicator, wherein said method comprises applying a stepwise regression subsequently to the LASSO.
  • a gene refers to a genomic DNA sequence which encodes a protein (coding sequence; CDS), or a microRNA or long non-coding RNA.
  • a genomic DNA sequence which encodes a protein also encodes the mRNA for the translation of said protein.
  • a microRNA is a small non-coding RNA molecule (containing about 22 nucleotides) that functions in RNA silencing and post-transcriptional regulation of gene expression.
  • Long noncoding RNAs long ncRNAs, lncRNA
  • lncRNA are a type of transcripts with typically more than 200 nucleotides which are not translated into proteins (but possibly into peptides). Still, the majority of long non-coding RNAs are likely to be functional, i.e. in transcriptional regulation.
  • the gene set of the invention does not comprise KCNK12.
  • the gene set of the invention comprises at least one, preferably at least 5, preferably at least 10, preferably at least 30, preferably all of ISPD, KCNK12, GNG2, SIRT7, GPATCH1, GRIA4, LINC01531, LOC101927577, NCOR2, WASF3, TRPV3, ACACA, GDNF, EFHC1, MYO10, COL23A1, TDRD1, ELOVL2, GNAI1, MAP4, CCDC179, KLF14, ST7, INPP5A, SIM1, SLC1A2, AS3MT, KSR1, DSCR6, IRF2, KCNS1, NRXN3, C11orf85, HBE1, FOXES, TMEM136, HOXD13, LOC375196, PANK1, MIR107, COL5A1, PBX4, ZNF140, GALNTL6, NUP107, LOC100507250, MTRNR2L5, C17orf82, MKLN1, FURIN, KLHL42, MO
  • said gene set is obtained by selecting from the ensemble of genomic DNA sequences those which encode a protein, or a microRNA or long non-coding RNA, wherein said ensemble of genomic DNA sequences is comprised in the age indicator obtained by the method for determining an age indicator, wherein said method comprises applying a stepwise regression subsequently to the LASSO.
  • the ensemble of genomic DNA sequences according to the invention comprises at least one, preferably at least 4, preferably at least 10, preferably all of cg11330075, cg00831672, cg27320127, cg27173374, cg14681176, cg06161948, cg08224787, cg05396610, cg15609017, cg09805798, cg19215678, cg12333719, cg03741619, cg03230469, cg19851481, cg10543136, cg07291317, cg26430984, cg16950671, cg16867657, cg13973351, cg16781885, cg04287203, cg27394136, cg10240079, cg02536625, and cg23128025.
  • said ensemble of genomic DNA sequences is comprised in the age indicator obtained by the method for determining an age indicator, wherein said method comprises applying a stepwise regression subsequently to the LASSO, and wherein each coefficient of said genomic DNA sequences comprised in said age indicator has an absolute value of more than 20.
  • the ensemble of genomic DNA sequences according to the invention comprises at least one, preferably at least 4, preferably all of cg11330075, cg00831672, cg27320127, cg10240079, cg02536625, and cg23128025.
  • said ensemble of genomic DNA sequences is comprised in the age indicator obtained by the method for determining an age indicator, wherein said method comprises applying a stepwise regression subsequently to the LASSO, and wherein each coefficient of said genomic DNA sequences comprised in said age indicator has an absolute value of more than 40.
  • the genomic DNA sequences comprised in the ensemble of genomic DNA sequences according to the invention are the full sequences and not the fragments thereof.
  • the ensemble of genomic DNA sequences according to the invention comprises the complementary sequences thereof in addition and/or in place of said ensemble of genomic DNA sequences.
  • a genomic DNA sequence refers to the sequence as described and/or the reverse complementary sequence thereof. The skilled person can easily judge if the sequence as described or the reverse complementary sequence thereof should be used. By default, and for most applications, the sequence as described is to be used, but for some applications, for example, for determining the methylation level of said sequence with a probe, the complementary sequence thereof is used for the probe.
  • the gene set of the invention comprises at least one, preferably at least 5, preferably at least 10, preferably at least 20, preferably all of:
  • MAP4 microtubule associated protein 4
  • PRKCZ protein kinase C zeta
  • GRIA4 glutamate ionotropic receptor AMPA type subunit 4
  • ST7 suppression of tumorigenicity 7
  • PRKCH protein kinase C eta
  • CACNA1D calcium voltage-gated channel subunit alpha1 D
  • DAP death associated protein
  • TRPV3 transient receptor potential cation channel subfamily V member 3
  • furin paired basic amino acid cleaving enzyme (FURIN), acetyl-CoA carboxylase alpha (ACACA), G protein subunit alpha i1 (GNAI1), solute carrier family 1 member 2 (SLC1A2), phosphodiesterase 4C (PDE4C), ELOVL fatty acid elongase 2 (ELOVL2), nuclear receptor corepressor 2 (NCOR2), endothelial PAS domain protein 1 (EPAS1), G protein subunit gamma 2 (GNG2)
  • said gene set is obtained from further filtering the gene set of the invention on genes which encode a protein whereof the level and/or activity can be determined with an available assay.
  • said gene set is further enriched for candidate drug targets.
  • the method for determining an age indicator according to the invention and the ensemble of genomic DNA sequences according to the invention are tightly linked and are based on a common inventive concept.
  • the description and definition of the ensemble of genomic DNA sequences according to the invention herein can be used to further specify the age indicator and/or the reduced training data set of the invention, both of which comprise an ensemble of genomic DNA sequences.
  • said age indicator and/or reduced training data set can be used to further specify the method for determining an age indicator and/or the method for determining the age of an individual.
  • the ensemble of genomic DNA sequences according to the invention which may be comprised in the age indicator of the invention, is preferably obtained by the method for determining an age indicator according to the invention.
  • this also applies to the gene set of the invention which preferably is selected from the ensemble of genomic DNA sequences according to the invention.
  • the invention relates to an age indicator obtained by the method for determining an age indicator according to the invention, and/or an ensemble of genomic DNA sequences comprised in said age indicator obtained by said method.
  • the invention relates to an age indicator as described in the Examples herein.
  • the age indicator obtained by the method for determining an age indicator and/or the ensemble of genomic DNA sequences comprised therein the same applies as is described herein for uses of the ensemble of genomic DNA sequences and/or the gene set according to the invention, in particular in a method for diagnosing the health state and/or the fitness state of an individual and/or in an in silico and/or in vitro screening method for identifying a molecule which affects ageing.
  • the invention relates to a method for diagnosing the health state and/or the fitness state of an individual comprising a step of providing the ensemble of genomic DNA sequences according to the invention, or the gene set according to the invention.
  • the health state comprises the state of at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer, wherein the state indicates the absence, presence, or stage of the disease or the phenotype associated with a disease.
  • the health state is preferably related to ageing.
  • a phenotype associated with an ageing-related disease refers preferably to at least one symptom of an ageing-related disease. Furthermore, an ageing-related diseases or cancer or a phenotype associated therewith, usually progresses is certain stages. Thus, herein, an ageing-related diseases or cancer or a phenotype associated therewith, can be absent or present, or be in a certain stage.
  • the ageing-related disease is Alzheimer's disease, Parkinson's disease, atherosclerosis, cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension, Age-Related Macular Degeneration and/or Benign Prostatic Hyperplasia.
  • the fitness state comprises the blood pressure, body weight, level of immune cells, level of inflammation and/or the cognitive function of the individual.
  • the health state and/or fitness state of an individual relates to his biological age.
  • the age of the individual which is determined according to the present invention describes said biological age and/or said health state and/or fitness state better than does the chronological age of said individual.
  • diagnosing the health state and/or fitness state of an individual is complementary to diagnosing one specific disease and/or health/fitness parameter.
  • diagnosing the health state and/or fitness state may provide a holistic or integrated perspective on the individual. For example, in case the diagnosis is rather negative, it may be indicated that the individual changes his life style and/or his environment.
  • diagnosing the health state and/or fitness state is particularly useful for evaluating if a certain medical treatment or change in the life style or environment of an individual has improved the overall health state and/or fitness state of the individual. It is obvious that the overall health state and/or fitness state of an individual, in particular when related to ageing, is a crucial factor for the wellbeing of said individual.
  • the method for diagnosing the health state and/or the fitness state according to the invention may allow diagnosing how young or old the individual biologically is.
  • the method for diagnosing the health state and/or the fitness state of an individual further comprises a step of determining the methylation levels of the genomic DNA sequences in a biological sample of said individual comprising said genomic DNA sequences.
  • the method for diagnosing the health state and/or the fitness state of an individual according to the invention comprises the medical application and/or the non-medical application of said method.
  • the invention relates to an in silico and/or in vitro screening method for identifying a molecule which affects ageing comprising a step of providing the ensemble of genomic DNA sequences according to the invention, or the gene set of the invention.
  • the molecule ameliorates, prevents and/or reverses at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer when administered to an individual.
  • said screening method is an in vitro method.
  • the prevention of an ageing-related disease and/or the phenotype associated therewith relates to the maintenance of its absence; the amelioration relates to the slowed down progression through the stages, the maintenance of a stage and/or the regression to an earlier stage; and the reversion relates to the regression to an earlier stage, preferably to the regression to the absence of the disease and/or the phenotype associated therewith.
  • cancer is a preferred ageing-related disease.
  • the screening method of the invention further comprises a step of determining the DNA methylation level of at least one of the genomic DNA sequences comprised in the ensemble of genomic DNA sequences and/or at least one of the genes comprised in the gene set.
  • the identified molecule increases and/or decreases the DNA methylation level of at least one of said genomic DNA sequences or genes in an individual when administered to said individual.
  • the DNA methylation levels are altered such that they are associated with a younger chronological age than before alteration.
  • the ensemble of genomic DNA sequences or the gene set according to the invention can be used for screening molecules, i.e. drug candidates, which alter the methylation state of said sequences or genes in a way which is associated with a younger chronological age than before alteration.
  • drug candidates which alter the methylation state of said sequences or genes in a way which is associated with a younger chronological age than before alteration.
  • the drug should decrease the methylation level of said genomic DNA sequence.
  • the drug should increase the methylation level of said genomic DNA sequence.
  • the screening method of the invention wherein the gene set of the invention is provided, further comprises a step of determining the activity of at least one protein encoded by the gene set.
  • said gene set only comprises genes which encode a protein.
  • the identified molecules inhibit and/or enhance the activity of at least one protein encoded by the gene set.
  • the protein activities are altered such that they are associated with a younger chronological age than before alteration.
  • the drug should decrease/inhibit the activity of said protein.
  • the drug should increase/enhance the activity of said protein.
  • the activity of a protein also encompasses the level of said protein, in particular of its active form.
  • the invention relates to a chip comprising the ensemble of genomic DNA sequences according to the invention, or the gene set of the invention as spots, wherein each sequence is contained in a separate spot.
  • the chip is a microarray chip.
  • the invention relates to a kit comprising
  • said primer pair is used for a polymerase chain reaction (PCR).
  • Said primers may be DNA methylation specific or not.
  • said primers are used for a methylation specific PCR method.
  • the DNA methylation levels may be determined by assaying the amplified PCR products, for example by sequencing or by comparing the quantity of the products obtained by different PCRs with primers binding to either methylated or unmethylated sequences.
  • said probe is used for a hybridization method, for example an in-situ hybridization method, or a microarray method.
  • the primer or probe specifically binds to either methylated or unmethylated DNA, wherein unmethylated cytosines have been converted to uracils.
  • conversion of unmethylated cytosines to uracils is done preferably by bisulfite treatment.
  • the kit further comprises a container for biological material and/or material for a buccal swab.
  • the kit further comprises material for extracting, purifying and or amplifying genomic DNA from a biological sample, wherein the material is a spin column and/or an enzyme.
  • the kit further comprises hydrogen sulfite.
  • the invention relates to the use of the chip of the invention and/or the kit of the invention for determining the DNA methylation levels of at least one of the genomic DNA sequences comprised in the ensemble of genomic DNA sequences according to the invention and/or one of the genes comprised in the gene set of the invention.
  • the invention relates to the use of the chip of the invention and/or the kit of the invention for diagnosing the health state and/or the fitness state of an individual.
  • the invention relates to the use of the chip of the invention and/or the kit of the invention in an in silico and/or in vitro screening method for identifying a molecule which affects ageing.
  • diagnosing of the health state and/or the fitness state of an individual and the in silico and/or in vitro screening method for identifying a molecule which affects ageing the same applies as has been described above in the context of a method for diagnosing the health state and/or the fitness state of an individual and the in silico and/or in vitro screening method for identifying a molecule which affects ageing.
  • the invention relates to a data carrier comprising the age indicator of the invention, the ensemble of genomic DNA sequences according to the invention, and/or the gene set of the invention.
  • the kit and/or the data carrier of the invention further comprises a questionnaire for the individual of whom the age is to be determined, wherein the questionnaire can be blank or comprise information about said individual.
  • the invention further relates to the following further aspects and embodiments.
  • the invention relates to a method of age determination of an individual based on the levels of methylation of genomic DNA sequences found in the individual, comprising the steps of preselecting from genomic DNA sequences having levels of methylation associable with an age of the individual a set of genomic DNA sequences; determining for a plurality of individuals levels of methylation for the preselected genomic DNA sequences; selecting from the preselected set an ensemble of genomic DNA sequences such that the number of genomic DNA sequences in the ensemble is smaller than the number of genomic DNA sequences in the preselected set, wherein the ages of the individuals can be calculated based on the levels of methylation of the sequences of the ensemble, and a statistical evaluation of the ages if calculated indicates an acceptable quality of the calculated ages; determining in a sample of biological material from the individual levels of the methylation of the sequences of the ensemble; calculating an age of the individual based on levels of the methylation of the sequences of the ensemble,
  • an ensemble of genomic DNA sequences is initially used, selected from a number of genomic DNA sequences having levels of methylation associable with an age of the individual; typically, the number of genomic DNA sequences in the ensemble is smaller than the number from which they are selected; then, methylation levels are obtained for the genomic DNA sequences of the ensemble, and from these an age is determined.
  • the composition of the ensemble and/or the way to determine an age based on the methylation levels obtained for the genomic DNA sequences of the ensemble is repeatedly altered based on additional information generated or gained during the series of determinations, in particular based on the methylation levels additionally determined.
  • the determination of an age will be based on an evaluation of methylation levels of specific genomic DNA sequences (or CpG loci) from a plurality of individuals, wherein the plurality of individuals comprises the exact individual, for whom the age is to be determined, although that need not be the case.
  • such an adaption of the ensemble and/or of the (best) way to determine an age based on the respective methylation levels obtained for the genomic DNA sequences of an ensemble currently considered may be altered with every further individual for whom methylation levels and preferably the chronological age are known. Sometimes, this might not be done for every individual, but only for some of these individuals.
  • the adaption could be effected only after the levels of methylation of genomic DNA sequences have been determined for a plurality of more than one additional individual such as 5, 8, 10, 20, 50 or 100 individuals. This would be particularly advantageous where the effort of statistical evaluation to either select certain genomic DNA sequences into an ensemble and/or to determine the best way of age determination based on the methylation levels of certain genomic DNA sequences is substantive.
  • the quality according to a (statistical) measure is not acceptable simply because the (statistical) measure indicates that the size of a reference plurality of individuals is smaller than a certain number, for example smaller than the overall number of all individuals for whom methylation levels have been determined and/or for whom methylation levels for the selected genomic DNA sequences have been determined and the chronological age is also known.
  • the methylation levels can be stored together with additional information about the individuals such as their chronological age (if known), so that the stored information can be used later on in a statistical (re-)evaluation. Accordingly, it is possible to gather such methylation level information for a plurality of additional individuals prior to reiterating the ensemble and/or the best way.
  • the invention suggests in one embodiment to improve a determination of an unknown age based on a statistical evaluation of measurements that themselves will yield the unknown result to be determined. Surprisingly, this is not contradictory in itself as by including such information in a reference group, overall improvements of the reliability of the method can be achieved. Accordingly, it has been found that a self-learning approach can be easily implemented.
  • the age determined by the method should, for a large group of individuals, correspond to the average of their chronological ages. Note that the age determined will be a biological age or at least be closer to a biological age, which may be different from the chronological age and will oftentimes only be useful as it varies vis-à-vis the chronological age, because then, it can be determined whether or not a particular individual is aging faster than average.
  • the method can be concluded or re-worded to relate to a method of establishing an age difference between a biological and a chronological age known or to assess differences between biological ages obtained by difference measurements and/or methods.
  • a preselection can be made by choosing a specific method of determination of methylation levels such as those provided for example by IlluminaTM and/or by choosing DNA chips that have a limited collection of spots that each can be used for determination of only one or some but not all genomic DNA sequences found in the individual and having levels of methylation associable with an age. Hence, the decision to use a specific detection method is an implicit preselection.
  • a preselection can be considered to have been made if only data derived in such a manner is evaluated, i.e. if data is evaluated from less than the full app. 28 million sites constitutes the basis of the ensemble and/or set of the preselected set.
  • the preselected set will be significantly smaller than 28 million different genomic DNA sequences.
  • commercially available methods allow determination of levels of methylation of 800,000 (800000) or more different genomic DNA sequences, it will be understood that methods using chips that allow determination of levels of methylation for only a very limited number of different genomic DNA sequences using a collection of specific sites or “spots” are significantly cheaper to use in determination of an age of an individual.
  • chips can be used that allow determination of levels of methylation of only one or a few thousand different genomic DNA sequences, preferably even less, in particular not more than 1000 CpG loci, preferably 500 different genomic DNA sequences or CpG loci, preferably less than 200 different genomic DNA sequences or CpG loci, preferably not more than 150 different genomic DNA sequences or CpG loci.
  • the composition of the ensemble may either only be altered in that certain genomic DNA sequences that previously had been considered are disconsidered after the reiteration and/or in that the best way to determine an age based on the methylations levels obtained for the genomic sequences of the ensemble itself is altered, for example where regression coefficients obtained from a multivariate (linear) correlation of methylation levels obtained for the genomic DNA sequences of the ensemble with a chronological age of individuals are changed. Also, it would be possible to carry out a determination of levels of methylation of further sequences prior to re-iteration.
  • each determination of levels of methylation of individuals is possible to include in each determination of levels of methylation of individuals (some) more genomic DNA sequences (or CpG loci) than those currently constituting part of an ensemble, for example about or at least 10 or about or at least 20 or about or at least 50 more sequences or CpG loci.
  • the number of genomic DNA sequences having levels of methylation associable with an age of the individual and determined for each individual or some individuals without constituting part of a current ensemble will normally be rather small. For example, it is possible to determine the levels of methylation for genomic DNA sequences currently not constituting part of the ensemble for not more than 5 times the number of genomic DNA sequences currently constituting part of the ensemble. Accordingly, where the ensemble for example comprises 100 different genomic DNA sequences, the overall number of different genomic sequences will usually be less than 500. Typically, there are even smaller numbers of additional genomic DNA sequences or CpG loci.
  • the additional genomic DNA sequences for which levels of methylation associable with an age are determined, although the respective genomic DNA sequences do not constitute part of an ensemble of genomic DNA sequences from which the age is determined is smaller than 400, preferably smaller than 300, in particular smaller than 100 and in particular less than 60, 50 or 40 CpG loci.
  • the ratio of genomic DNA sequences, not constituting part of the ensemble over genomic DNA sequences in the ensemble is preferably smaller than 5, preferably smaller than 4, preferably smaller than 3, preferably smaller than 2. It is noted that the additional sequences that are currently not constituting part of an ensemble but are used to provide additional levels of methylation only in case these might be helpful in a re-iteration will typically be carefully selected as well. This can be done in the preselection.
  • CpG loci might be selected to the set that have methylations levels correlating well with methylation levels of CpG loci that, while also selected into the ensemble, have a very low overall methylation or a high variance.
  • CpG loci could be included known to be indicative for specific adverse lifestyles even though such loci would not be predominant in a statistical multivariate analysis.
  • CpG loci could be selected additionally that are relevant to subsets of an initial reference group.
  • the exact numbers of the entire set and/or the ensemble will depend on the availability of affordable measurement methods such as sufficiently cheap chips. Also, data processing costs may be prohibitive. It may be preferred to use a chip adapted to determine levels of methylation of genomic DNA sequences having no more than 1000, 500, 200 spots each adapted to be used in determination of methylation levels of a different CpG locus.
  • this chip comprises at least one spot, preferably at least 10, in particular at least 20, 30, 40, 50 60, 70, 80, 90 or 100 and in particular all spots allowing determination of levels of methylation of one or more, in particular at least 20, 30, 40, 50 60, 70, 80, 90 or 100 and in particular all of the following genomic DNA sequences or CpG loci: cg11330075, cg25845463, cg22519947, cg21807065, cg09001642, cg18815943, cg06335143, cg01636910, cg10501210, cg03324695, cg19432688, cg22540792, cg11176990, cg00097800, cg09805798, cg03526652, cg09460489, cg18737844, cg07802350, cg10522765, cg12548216, cg008763
  • each of said genomic DNA sequences or CpG loci is comprised in a separate spot of said chip.
  • one spot of said chip is defined by one of said genomic DNA sequences or CpG loci. It will be obvious that it is useful that at least a plurality of those CpG loci are referred to when measuring the methylation level using a chip.
  • all of the above CG loci will constitute part of a set of preselected genomic DNA sequences having levels of methylation associable with an age of the individuum, so that an ensemble of genomic DNA sequences can be easily obtained comprising either all of the above-listed CG loci or, in a preferred embodiment, at least a number or fraction of the above-listed CG loci.
  • said chip may be used for determining the DNA methylation levels of a set of genomic DNA sequences, in particular the genomic DNA sequences comprised in the reduced training data set according to the invention.
  • the CpG Loci will additionally comprise cg27320127, the last CpG loci being known inter alia from WO2012/162139.
  • the CpGs identified above are identified using IlluminaTM methylation probe IDs.
  • the chip will comprise a low overall number of spots allowing determination of levels of methylation of the following genomic DNA sequences, in particular less than 1600 spots, in particular less than 800 spots, in particular less than 400 spots, preferably less than 200 spots.
  • At least 10, preferably 20, particularly preferred 50, 100 and in particular all of the above-listed CpG loci believed to be novel over those known in the art may constitute part of a preselected set of genomic DNA sequences having levels of methylation associable with an age of the individuum and in particular comprising no more than 5000, in particular no more than 2000, in particular no more than 1000, in particular no more than 250 genomic DNA sequences or CpG loci and/or constituting a fraction of at least 10% of the overall number of genomic DNA sequences in a preselected set, preferably at least 10% thereof, and particularly preferred at least 15%, 20%, 25%, 33%, 50%, 66%, 75%, 80%, 100%. So, in preferred cases the CpG loci listed and newly disclosed herein as being relevant will constitute a significant part of the ensemble.
  • the overall number of CG loci considered in a set from which the ensemble is to be selected will be dependent on the number of different loci measurable easily and, in a cost-effective manner, according to a respective state of the art.
  • prices of DNA chips having oligonucleotides that bind in a measurement process to DNA fragments comprising the respective CpG loci vary strongly with a number of different sites, with the costs dropping significantly from chips having 1000 or more sites to chips having 500, 384, 192 or 96 different sites.
  • the numbers of 96 or 384 while in no way restricted, refer to numbers frequently used in current laboratory procedures. It has already been stated that usually the step of preselecting can be considered to have been effected once it has been decided to use not all CpG loci known in the human being but only those easily accessible. Such a step of preselection could thus be made by a referring to the data set comprising only a correspondingly small number of methylation levels.
  • determining in a sample of biological material from an individual levels of the methylation of the sequence of the ensemble can be done by referring to measurements that already have been done on the sample. Accordingly, a determination of levels of the methylation of certain sequences could be effected by opening a corresponding data file. The same holds for selecting from the preselected set an ensemble of genomic DNA sequences in a specific manner. This selection should be considered made in case reference is being had to a data base comprising such an ensemble determined by a preceding analysis of reference data from individuals.
  • the number of genomic DNA sequences in the set and/or in the plurality is rather large, for example because they comprise more than 5, in particular more than 10, in particular at least 50 different genomic DNA sequences.
  • the number of individuals in the group is rather large as well, that is comprising preferably at least 10, preferably at least 50, in particular at least 100, in particular at least 200, and in a preferred embodiment at least 1000 individuals.
  • mathematical analysis in particular statistical analysis is needed to determine the best way of calculating an age of an individual based on the levels of the methylation determined.
  • a “best” way of such calculation may not be the absolute best way but can refer to some very good way.
  • a way of determination may be stated to be a “best” way even though either the calculations are particularly simple and/or because a local extreme of statistical functions has been used instead of an absolute extreme.
  • the calculation of an age of an individual based on levels of the methylation of the sequences of the ensemble will be done in a manner where values relating to the level of methylation such as percentages are used to calculate the age based in a manner using also regression coefficients from a multivariate regression, and in particular from a multivariate linear regression.
  • Calculating a measure such as a statistical measure can be effected in different ways. For example, it can be determined whether or not the levels of the methylation of the sequences themselves should be considered reliable. Where levels are exceptionally low, it might not be advisable to use the respective sequences and/or levels of the methylation because, for example, an error in the determination might have occurred (e.g.
  • calculating a statistical measure of the quality of the age calculated could take into account whether or not a known chronological age deviates from the calculated biological age significantly more than the entirety of deviations obtained for the reference set and/or more than a plurality of other individuals for whom the levels of the methylation of the sequences of the ensemble has been measured.
  • a difference can be considered to be significantly larger, if the significance is at least 2 ⁇ , 3 ⁇ , 4 ⁇ , 5 ⁇ or 6 ⁇ .
  • the statistical measure of quality could be estimated by determining whether or not the reference set of individuals is sufficiently large. This would not be the case for example where a regression is carried out having a Spearman correlation of less than 0.85, preferably less than 0.90, preferably less than 0.91 and preferably 0.92 with a mean average error (MAE) of more than 6 years, preferably more than 5 years, in particular more than 4 years. It will be understood that it is also possible to estimate a confidence interval for each separate age calculated and that calculating a statistical measure might include the determination of a confidence interval of an age calculated. However, calculating a statistical measure of the quality of the age calculated might also be done easier, for example by determining whether the underlying reference group is large enough.
  • the quality is not high enough if the group is considered to be too small. This can be the case if either the number of individuals in the reference group overall is too low and/or if the number of individuals in the reference group is too low in view of the number of genomic DNA sequences or CpG loci respectively in the preselected set of genomic DNA sequences or in the selected ensemble.
  • the quality of an age calculated will not be sufficiently high in case not all individuals for whom methylation levels have been determined or not all individuals having certain properties such as being smokers or being female and so forth have been referred to when determining a best way of estimating and calculating an age.
  • the (statistical) measure would be the number of members in the reference group vis-à-vis the number of individuals for whom levels of methylation and, where applicable, additional information are available.
  • a calculation of such difference could be done by determining that new data has not been entered into the reference group even prior to calculation of an age of the individual. Then, it should be noted that while at least the age of the individual is outputted in case the quality thereof is judged to be acceptable, it is also possible to output the age even where the quality of the calculation is considered dubious or insufficient. For example, it might be useful to output the age of an individual nonetheless because this allows an operator to check whether any specific problem can be detected that easily explains why the quality of the calculated age is to be considered subpar.
  • a plurality of ensembles of CpG loci are defined based on the set and one of these ensembles is selected based on specific information either derived from one or more specific methylation level of CpG loci analyzed and/or an additional information provided independently thereof.
  • Some of the CpG loci in the preselected set can be chosen such that a specific ensemble can be selected. Such provision and/or selection of a specific ensemble from several ensembles should be considered inventive per se. Also, it would be possible to output the age calculated with an explanation to the individual and offer a refund as standard or guaranteed qualities have not been achieved.
  • Amending the group of individuals usually would be done by including the one or more individuals for whom individual levels of methylation have additionally been determined. However, it would also be possible to exchange individuals or amend the group of individuals by splitting the group and so forth. For example, a case might occur where an initial group of individuals has been rather small so that a differentiation between smokers and non-smokers, males and females, young and old, persons drinking alcohol or not was not advisable, feasible or reasonable. Then, after some time, a large number of measurements will have been carried out and, in some cases, the additional properties such as individuals being smokers or not will have been determined so that then the group can be amended by adding one or some individuals based on their property and by splitting the groups according to such properties.
  • the levels of methylation will change in a large number of living organisms in a manner relating to the age of the organism.
  • the method of age determination will be used to determine the age of mammals, in particular primates, in particular human beings. Still, at least a rough estimate of age might be useful, e.g. for other living beings where trading animals that are particularly expensive.
  • the individual is a human.
  • this will then also hold for the individuals of the reference group. It has already been indicated above that the numerous steps listed above will require extensive calculations. Therefore, implementing these steps in an automated manner to be executed by a computer is vital. It should be noted that for cases where at least 20 different genomic DNA sequences are considered in the set or the ensemble and where at least 20, preferably 100 individuals form the reference group, calculations without computer implementation are expected to be particularly error-prone so that the results in their entirety must be considered completely useless and unreliable. Also such calculations would neither be affordable in view of costs of computation done by a human being nor acceptable by any individual having to wait for a result. Therefore, executing at least one and preferably all of the calculation and evaluation steps by computers are considered vital.
  • methylation sequencing/bisulfate sequencing PCR-methods, in particular at least one of methylation specific PCR (MSP), real-time methylation specific PCR, quantitative methylation specific PCR (QMSP), COLD-PCR, PCR using a methylated DNA-specific binding protein, targeted multiplex PCR, real-time PCR and microarray-based PCR, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), methylation-sensitive single-strand conformation analysis, methyl-sensitive cut counting (MSCC), base-specific cleavage/MALDI-TOF, e.g.
  • MSP methylation specific PCR
  • QMSP quantitative methylation specific PCR
  • COLD-PCR COLD-PCR
  • HRM high resolution melting analysis
  • MS-SnuPE methylation-sensitive single-strand conformation analysis
  • MSCC methyl-sensitive cut counting
  • base-specific cleavage/MALDI-TOF e.
  • Agena combined bisulfate restriction analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), micro array-based methods, bead array-based methods, pyrosequencing, direct sequencing without bisulfate treatment (nanopore technology).
  • COBRA combined bisulfate restriction analysis
  • MeDIP methylated DNA immunoprecipitation
  • micro array-based methods bead array-based methods
  • pyrosequencing direct sequencing without bisulfate treatment
  • methylation sequencing/bisulfate sequencing methylation specific PCR
  • MSP methylation specific PCR
  • QMSP quantitative methylation specific PCR
  • COLD-PCR base-specific cleavage/MALDI-TOF, e.g. Agena, micro array-based methods, bead array-based methods, pyrosequencing.
  • the group of individuals for whom levels of methylation are initially determined is sufficiently large to obtain calculated ages that remain sufficiently stable even if the self-learning still leads to significant process.
  • an initial training of the process by reiterating the ensemble selection and/or the best way of obtaining results should relate on at least 50 individuals, so as to have sufficiently stable values for initial reference, it usually is preferred to have larger numbers such as 100 or 200 individuals in a reference group before starting actual measurements.
  • reiterating the composition of the ensemble and all the best way of calculating an age therefrom can be postponed after a sufficiently large number of additional individuals can be additionally considered or added to the reference group.
  • the number of genomic DNA sequences in the preselected set can be made rather small while still allowing to amend the ensemble in a useful manner.
  • the preselected set will on the one hand comprise at least 90 CpG loci, preferably at least 100 CpG loci, particularly preferred at least 140 CpG loci, in particular at least 150 CpG loci.
  • the preselected set shall not be excessive for a variety of reasons. First of all, determination of methylation levels of CpG loci is more costly and more complex if more CpG loci are to be examined with respect to the methylation level.
  • a method relying on a large number of CpG loci is costly and reducing the number of CpG loci in an ensemble or in a preselected set does reduce the cost significantly.
  • the data processing is significantly simplified if less CpG loci need to be considered. This holds both for a reiteration of the CpG loci in the ensemble and for the best way of processing methylation obtained for such loci. It is noted that generally, the calculation expands a particular of reiterating the ensemble or best way should be considered to grow in a highly nonlinear manner with a number of genomic DNA sequences considered. Therefore, it is preferred from a data analysis perspective as well to reduce the number of CpG loci considered.
  • methylation levels determined in an electronic, automated manner e.g. by establishing an electronic record or file for the methylation levels that can be used when processing the data even where such data processing is not immediately done after determination of methylation levels; not using computer interfaces for data transmission between the final stage used for obtaining the methylation levels from the samples and the stage used for data analysis would introduce a source of errors that must be considered unacceptable.
  • the method generally is a computer implemented method having computer implemented steps and that at least some steps must necessarily be executed using a computer.
  • the selected ensemble will have a number of CpG loci rather small, in particular comprising less than 150 CpG loci, in particular less than 110 CpG loci, in particular less than 100 CpG loci, and in particular less than 90 CpG loci, in particular less than 80 CpG loci, and in particular less than 70 CpG loci.
  • the ensemble should not be too small. Otherwise, there is a risk that the age or the deviation of the age determined vis-à-vis the chronological age is affected by measurement errors, an insufficient database in the reference group and so forth. Therefore, in some embodiments, it is advisable to include at least 30 CpG loci in the ensemble, preferably at least 50 CpG loci and in particular at least 60 CpG loci.
  • the number of members in the ensemble after reiteration may be different from the number of members in the ensemble prior to reiteration.
  • the number of CpG loci in the ensemble may vary optionally, i.e. a mere replacement of one or more CpG loci and the ensemble against one or more other CpG loci in the ensemble is not forbidden.
  • methylation levels are used by considering values that vary between 0% for a minimum methylation of a given CpG locus and 100% of a given CpG locus, the later value being used when the methylation level corresponds to the maximum methylation possible for a given CpG locus.
  • the methylation level of values are centered and normalized.
  • a value between 0 and 1 could also be used. While other ranges of values could be used, using values between 0 and 1 or 0% and 100% is particularly intuitive when assessing results and so forth.
  • the age of the individual calculated is outputted prior to re-selection of the ensemble independent of the judgement of quality of the measurement.
  • an embodiment exists, wherein if the age of the individual calculated is judged to not be acceptable; and an age is outputted only after a re-selection of the ensemble of genomic DNA sequences has been effected and after an age has been recalculated for the reselected ensemble.
  • LASSO and elastic net are different regression methods, at least because LASSO does not comprise a Ridge regression and/or in elastic net, the L1 regularization parameter is not 1.
  • such a kit will comprise at least a container for biological material of an individual obtained and/or prepared in a manner allowing determination of age according to a method as disclosed herein; the kit also comprising an information carrier carrying information relating to the identification of the patient or individual; the kit further comprising either instructions to execute a method of the invention and/or instructions how to have such a method of the invention executed, e.g. by sending in the probe to a specific lab with a voucher, and/or to provide data for the production of a data carrier comprising age related data determined by a method according to the present invention and/or to provide a data carrier comprising age related data determined by a method according to the present invention.
  • the biological age of an individual might be determined by using an ensemble of CpG loci that is particularly useful for non-smokers; this might be useful where the individual has indicated to be a non-smoker.
  • a case might occur where a non-smoker has been forced to passively smoke over a long period, for example because of growing up with smoking parents.
  • the methylation levels of specific CpG loci might have been subjected to substantive change vis-à-vis a true non-smoker so even if otherwise, a correct biological age is determined, it might be useful to indicate to the individual that certain CpG methylation levels indicative of smoking behavior indicate that the person has suffered strongly from (passive) smoking.
  • the preselected set may include additional CpG loci that while not representative for a biological age in a large reference group might still be relevant for a specific individual.
  • a method of drug screening wherein a number of molecules are screened with respect to effecting aging comprising the steps of determining for specific CpG loci whether a molecule of the large number of molecules screened has a positive effect on the methylation levels of the CpG loci. This can be done in particular by a determination effected at least in part in-silico.
  • a method of age determination according to the present invention that after a first ensemble of genomic DNA sequences has been selected and ages are determined for a series of individuals, and wherein for at least some individuals of the series methylation levels of genomic DNA sequences additional to those in the ensemble are determined, the group of individuals is amended to include at least some individuals from the series and a determination is made as to whether the ensemble of genomic DNA sequences should be altered in view of methylation levels obtained for additional genomic DNA sequences that were determined for at least some individuals of the series.
  • the determination of a biological age is altered repeatedly during the course of measurements using more and more data obtained during in the series even if each single determination of the series yields an acceptable result that is a result that has a rather small and easily acceptable confidence interval.
  • the reiteration that is repeatedly executed may, as has been indicated before, relate to only the amendment of regression parameters obtained from a statistical analysis and used in the calculation of an age of an individual, using the methylation levels obtained for the individual or may decide that the ensemble overall should be altered, i.e. additional DNA sequences should be added and/or DNA sequences currently considered should be disconsidered.
  • the set should be carefully selected and a multiselection step for determining a useful preselection oftentimes may be advisable.
  • the methylation levels of genomic DNA sequences of a few hundred individuals could be measured for some 800,000 (800000) different genomic DNA sequences.
  • a few thousand genomic DNA sequences could be selected, for example in view of a principal component analysis determining the main components of the data set of methylation levels obtained versus the actual ages of the patient.
  • additional measurements could be effected for several hundred or more, e.g. a few thousand individuals and from the data set thus generated, several hundred genomic DNA sequences could be selected, for example of 384 DNA sequences that will have methylation levels detectable by a DNA chip having 384 different or oligonucleotide spots.
  • genomic DNA sequences could be made in view of a further principal component analysis, in view of the values of the respective methylation levels, in view of several methylation levels of different genomic DNA sequences being highly correlated and so forth.
  • the ensemble could be determined, but the determination of methylation levels can be determined for all of the remaining methylation DNA sequences without excessive costs.
  • the decision when deciding whether or not the ensemble or the best way of determining an age in view of methylation levels obtained should be altered, the decision is made based on a set of individuals as large as possible. Therefore, it is possible to provide additional data other than the methylation levels of the ensemble for at least some individuals in addition to the individuals of a presently used reference group. Then, a decision as to whether or not the ensemble or the best way of determining an age should be altered is made (also) in view of the methylation levels obtained for the additional individuals.
  • the information relating to the additional individuals is used in such a decision as to the best way of calculating the age or as to the selection of genomic DNA sequences into the ensemble or out of the ensemble by simply enlarging a given group of individuals.
  • One reason to exclude individuals from the reference group previously used could be in that a large number of additional individuals is added to the reference group and by doing so, when analyzing the entire group of both previous and added individuals, previously present individuals might be found to have methylation levels that now constitute statistical outliers.
  • a preselection has been made using a first detection method for detecting methylation levels
  • a first detection method for detecting methylation levels such as a detection method measuring the methylation levels of some 850000 CpG loci while the actual measurement is performed with a method that is capable of determining the methylation levels of only way less CpG loci, and the methylation levels for these CpG loci show a behavior different from the behavior of the methylation levels of the same CpGs in a cross comparison.
  • a first detection method for detecting methylation levels such as a detection method measuring the methylation levels of some 850000 CpG loci while the actual measurement is performed with a method that is capable of determining the methylation levels of only way less CpG loci, and the methylation levels for these CpG loci show a behavior different from the behavior of the methylation levels of the same CpGs in a cross comparison.
  • a deletion might be useful is if a sufficiently large number of individuals have finally been sampled that share a common property and the individual to be deleted from the reference group does not share this property. For example, it is possible to delete individuals that are obese from an initial reference group if after some time it is decided that the ensemble and best way of determining an age should be determined such that best results are obtained for perfectly trained athletes that are not obese.
  • judgment of the quality of a determined age is done in that a comparison is made with a known chronological age.
  • a confidence interval is known that can be taken as a measure of quality.
  • a very broad confidence interval might indicate that the determined age is unreliable.
  • the age determined does not deviate too far from ages of other individuals previously determined.
  • a large reference group has been examined and a new individual has a determined biological age that shows an aging behavior way faster or way slower than other individuals aging fast or slow, for whom previously data have been analyzed, it is not unlikely that an error has occurred, in particular if no additional factors influencing aging are known.
  • the age determined would be indicated to the individual because, even though it cannot be assured that the age determined is reliable, it might be advisable for the individual to act as if the age determined would be reliable. For example, where a particularly fast aging behavior previously not observed in a large group of individuals is observed, so that the quality of the high age relative to the actual chronological age cannot be assessed, it might be necessary for the individual to consult a medical doctor.
  • the invention relates to the following items:
  • the invention relates to the following items:
  • Item No. 79 relates to a method of age determination of an individual based on the levels of methylation of genomic DNA sequences found in the individual, comprising the steps of
  • the invention has been disclosing an item 80 relating to a method of age determination according to above listed, numbered item 79 wherein the individual is a human.
  • the invention has been disclosing an item No. 81 relating to a method of age determination according to one of the preceding above listed, numbered items, wherein at least one step is a computer implemented step,
  • the invention has been disclosing an item No. 82 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the levels of methylation of genomic DNA sequences found in the individual are measured by at least one of methylation sequencing/bisulfate sequencing, a PCR—method, in particular at least one of methylation specific PCR (MSP), real-time methylation specific PCR, quantitative methylation specific PCR (QMSP), COLD-PCR, PCR using a methylated DNA-specific binding protein, targeted multiplex PCR, real-time PCR and microarray-based PCR, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), methylation-sensitive single-strand conformation analysis, methyl-sensitive cut counting (MSCC), base-specific cleavage/MALDI-TOF, e.g.
  • MSP methylation specific PCR
  • QMSP quantitative methylation specific PCR
  • Agena combined bisulfate restriction analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), micro array-based methods, bead array-based methods, pyrosequencing, direct sequencing without bisulfate treatment (nanopore technology).
  • COBRA combined bisulfate restriction analysis
  • MeDIP methylated DNA immunoprecipitation
  • micro array-based methods bead array-based methods
  • pyrosequencing direct sequencing without bisulfate treatment
  • the invention has been disclosing an item No. 83 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the levels of methylation of genomic DNA sequences are measured by at least one of
  • the invention has been disclosing an item No. 85 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the group of individuals is amended by adding the individual to the group.
  • the invention has been disclosing an item No. 86 relating to a method of age determination according to one of the previous above listed, numbered items, wherein amending the group of individuals to include the individual comprises eliminating at least one other individual from the group, in particular in view of factors unrelated to their age and/or methylation levels of some or all of their genomic DNA sequences.
  • the invention has been disclosing an item No. 89 relating to a method of age determination according to the previous above listed, numbered item, wherein a determination is made to alter the ensemble based on methylation levels obtained for additional individuals if at least one or preferably several of the following conditions have been met:
  • the invention has been disclosing an item No. 90 relating to a method of age determination according to one of the previous above listed, numbered items, wherein judging whether or not the quality according to the statistical measure is acceptable or not comprises a statistical evaluation of the ages taking into account the known chronological ages of at least part of the individuals, in particular a statistical evaluation taking into account if a predicted age of a single individual deviates too far from a known chronological age of the individual, in particular vis-à-vis a known outlier behavior.
  • the invention has been disclosing an item No. 91 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the preselected set comprises at least 90 genomic DNA sequences, preferably at least 100 genomic DNA sequences, particularly preferred at least 140 genomic DNA sequences and/or the preselected set comprises less than 2000 genomic DNA sequences, in particular less than 500 genomic DNA sequences, in particular less than 350 genomic DNA sequences, in particular less than 170 genomic DNA sequences, in particular less than 150 genomic DNA sequences.
  • the invention has been disclosing an item No. 92 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the selected ensemble comprises at least 30 genomic DNA sequences, preferably at least 50 genomic DNA sequences, particularly preferred at least 60 genomic DNA sequences and/or the selected ensemble comprises less than 150 genomic DNA sequences, in particular less than 110 genomic DNA sequences, in particular less than 100 genomic DNA sequences, in particular less than 90 genomic DNA sequences, in particular less than 80 genomic DNA sequences, in particular less than 70 genomic DNA sequences.
  • the invention has been disclosing an item No. 93 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the reselected ensemble comprises at least 30 genomic DNA sequences, preferably at least 50 genomic DNA sequences, particularly preferred at least 60 genomic DNA sequences and/or the selected ensemble comprises less than 150 genomic DNA sequences, in particular less than 110 genomic DNA sequences, in particular less than 100 genomic DNA sequences, in particular less than 90 genomic DNA sequences, in particular less than 80 genomic DNA sequences, in particular less than 70 genomic DNA sequences.
  • the invention has been disclosing an item No. 94 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the number of genomic DNA sequences in the re-selected ensemble is different from the number of genomic DNA sequences in the initially selected ensemble.
  • the invention has been disclosing an item No. 95 relating to a method of age determination according to one of the previous above listed, numbered items, wherein at least one genomic DNA sequence included in the selected ensemble is not included in the genomic DNA sequences of the re-selected ensemble.
  • the invention has been disclosing an item No. 96 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the age is determined from a statistical analysis of the methylation levels of the genomic DNA sequences of the ensemble in view of known ages of individuals in the group, in particular by using coefficients obtained for respective genomic DNA sequences of the ensemble in a multiple linear regression of methylation level values against known ages of individuals in the group.
  • the invention has been disclosing an item No. 97 relating to a method of age determination according to one of the previous above listed, numbered items, wherein methylation level values are determined from methylation levels by centering and/or normalizing obtained levels and wherein the methylation level values are subjected to the statistical analysis.
  • the invention has been disclosing an item No. 98 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the age of the individual calculated is outputted prior to re-selection of the ensemble independent of the judgement of quality of the measurement.
  • the invention has been disclosing an item No. 99 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the age of the individual calculated is judged to not be acceptable and an age is outputted only after a reselection of the ensemble of genomic DNA sequences has been effected and after an age has been recalculated for the re-selected ensemble.
  • the invention has been disclosing an item No. 100 suggesting a method of age determination according to one of the previous above listed, numbered items, wherein the selection of genomic DNA sequences is based on a statistical analysis of values relating to methylation levels of genomic DNA sequences of the individuals, in particular a statistical analysis using at least one regression method for identification of relevant CpG loci, in particular at least one of a principal component analysis, a LASSO/elastic net regression and/or an XPG Boost method for identification of relevant CpGs.
  • the invention has been disclosing an item No. 101 relating to a kit comprising at least a container for biological material of an individual obtained and/or prepared in a manner allowing determination of age according to one of the preceding method above listed, numbered items; the kit also comprising an information carrier carrying information relating to the identification of the patient; the kit further comprising instructions to execute or how to have executed a method according to one of the preceding method above listed, numbered items and/or to provide data for the production of a data carrier comprising age related data determined by a method according to a previous method above listed, numbered item and/or to provide a data carrier comprising age related data determined by a method according to a previous method above listed, numbered item.
  • the invention has been disclosing an item No. 102 relating to a method of assessing a difference between a chronological age and a biological age, the method comprising determining an age based on methylation levels according to a method according to one of the preceding method above listed, numbered items and comparing the determined biological age to a known chronological age.
  • the invention has been disclosing an item No. 103 relating to a method of assessing a difference between a chronological age and a biological age according to the previous above listed, numbered items, wherein for a plurality of individuals a difference is determined, values of factors that may or may not affect the differences are determined for the plurality of individuals and factors having a large influence on the difference between a chronological age and the biological age in a large number of individuals are determined.
  • the invention has been disclosing an item No. 104 relating to a method of screening a number of molecules with respect to effecting aging comprising the steps of determining a number of genomic DNA sequences that correlate well to a biological age, in particular by referring to genomic DNA sequences selected for an ensemble in the method of above listed, numbered item 79, and determining whether a molecule of the number of molecules has a positive effect on the methylation levels of the genomic DNA sequences, in particular by an in-silico determination.
  • the invention has been disclosing an item No. 105 relating to a method of determination of an age of an individual based on an evaluation of methylation levels of selected genomic DNA sequences from a plurality of individuals, wherein the plurality of individuals comprises the individual.
  • the invention has been disclosing an item No. 106 relating to a chip comprising a number of spots, in particular less than 500, preferably less than 385, in particular less than 193, in particular less than 160 spots, adapted for use in determining methylation levels, the spots comprising at least one spot and preferably several spots specifically adapted to be used in the determination of methylation levels of at least one of cg11330075, cg25845463, cg22519947, cg21807065, cg09001642, cg18815943, cg06335143, cg01636910, cg10501210, cg03324695, cg19432688, cg22540792, cg11176990, cg00097800, cg09805798, cg03526652, cg09460489, cg18737844, cg07802350, cg10522765, cg12548216
  • the invention has been disclosing an item No. 107 relating to a method of determination of an age indicator for an individual in a series of individuals, the determination being based on levels of methylation of genomic DNA sequences found in the individual, wherein based on methylation levels of an ensemble of genomic DNA sequences selected from a set of genomic DNA sequences having levels of methylation associable with an age of the individuals an age indicator for the individual is provided in a manner relying on a statistical evaluation of levels of methylation for genomic DNA sequences of the plurality of individuals, characterized in that the age indicator for the individual is provided in a manner relying on a statistical evaluation of levels of methylation for genomic DNA sequences of a plurality of individuals which is different from the plurality of individuals that was referred to for a preceding statistical evaluation used for the determination of the same age indicator of an individual preceding in the series, the difference of plurality of individuals being caused in that a plurality of individuals used for the first statistical evaluations is amended at least by inclusion of at least one additional preced
  • a method of determination of an age indicator for an individual in a series of individuals based on levels of methylation of genomic DNA sequences is disclosed, wherein an ensemble of genomic DNA sequences is selected and an age indicator for the individual is provided in a manner continuously improving a statistical evaluation of previous measurements to obtain a better model.
  • FIG. 1 Performance of LASSO.
  • a set of 148 cg sites was determined as optimal. Shown are four plots referring to Lasso regression and its performances. In all four plots a vertical dotted line represents the automatic threshold chosen for the number of variables selected. All plots report mean values plus range intervals produced by 20 cross validation runs. The different axes show different model metrics according to the biglasso package. The two upper plots report sums of cross-validated errors and coefficient of determination (R 2 ), while the bottom two plots report two particular parameter from R implementation of LASSO regression: signal-to-noise ratio and ⁇ bs>. Details are in https://cran.rstudio.com/web/packages/biglasso/biglasso.pdf
  • FIG. 2 Performance of the age indicator obtained by LASSO and subsequent stepwise regression. Shown are the chronological age (actual age) and the determined age (predicted age) of 259 individuals of the training data set and 30 individuals of the test data set. No relevant or significant differences between training and test data set were observed. The shown coefficient of variation R 2 is based on the training and test data merged.
  • FIG. 3 Correlations of representative CpG sites with the chronological age. Individuals of training and test data merged were grouped based on their chronological age (>48 years, 25-48 years, and ⁇ 25 years; “old”, “mid” and “young”, respectively). The distributions of DNA methylation levels (“value”) are shown for 8 representative CpG sites per age group. The genes comprised in the CpG sites are annotated.
  • FIG. 4 Overlap of CG sites with the set of CG sites as described by Horvath in Genome Biology 2013, 14:R115.
  • the Venn diagram reports the amount of overlap between the set of 148 genomic DNA sequences (CpGs) determined herein by applying LASSO (IME-Cerascreen) and the 353 CpG List reported by Horvath in Genome Biology 2013, 14:R115. See also FIG. 5 .
  • FIG. 5 Overlap of CG sites determined herein by applying LASSO (IME-Cerascreen) and subsequent stepwise regression (IME_Cerascreen_8). Also shown is the overlap with the set of CG sites as described by Horvath in Genome Biology 2013, 14:R115. See also FIG. 4 .
  • LASSO IME-Cerascreen
  • IME_Cerascreen_8 stepwise regression
  • Example 1 Measuring CpG Methylation Levels of DNA from Biological Samples
  • Buccal cells were collected from a number of test persons with buccal swabs and genomic DNA was purified from the buccal cells using a QIAamp 96 DNA Swab BioRobot Kit (Qiagen, Hilden, Germany).
  • the purified genomic DNA was treated with sodium bisulfite using the Zymo EZ DNA Methylation Kit (Zymo, Irvine, Calif., USA). This treatment converts unmethylated cytosines to uracil, while methylated cytosines remain unchanged.
  • the fragmented, resuspended DNA samples were then dispensed onto an Infinium MethylationEPIC BeadChip (IlluminaTM) and the BeadChip was incubated overnight in the IlluminaTM Hybridization Oven to hybridize the samples onto the BeadChip by annealing the fragments to locus-specific 50mers that are covalently linked to the beads.
  • IlluminaTM Infinium MethylationEPIC BeadChip
  • Unhybridized and nonspecifically hybridized DNA was washed away and the BeadChip was prepared for staining and extension in a capillary flow-through chamber.
  • Single-base extension of the oligos on the BeadChip using the captured DNA as a template, incorporates fluorescent labels on the BeadChip and thereby determines the methylation level of the query CpG sites.
  • the BeadChip was scanned with the iScan System, using a laser to excite the fluorophore of the single-base extension product on the beads and recording high resolution images of the light emitted from the fluorophores.
  • the data was analyzed using the GenomeStudio Methylation Module (IlluminaTM), which allows the calculation of beta-values for each analyzed CpG.
  • IlluminaTM GenomeStudio Methylation Module
  • the methylation levels of more than 850′000 (850000) different IlluminaTM defined CpGs were measured per sample and person and a numerical value for each methylation level of the more than 850′000 (850000) different CpGs was provided. This was done for a large number of samples, each sample from a different individual. The numerical values have been normalized such that 0 corresponds to minimum methylation possible for a CpG and 1 corresponds to the maximum methylation for the CpG. Of note, 1 also corresponds to 100% or full methylation.
  • Example 2 Measuring CpG Methylation Levels by Base-Specific Cleavage/MALDI-TOF (Agena)
  • Buccal cells were collected from a number of persons with buccal swabs and genomic DNA was purified from the buccal cells using a QIAamp 96 DNA Swab BioRobot Kit (Qiagen, Hilden, Germany).
  • the purified genomic DNA was treated with sodium bisulfite using the Zymo EZ DNA Methylation Kit (Zymo, Irvine, Calif., USA). This treatment converts unmethylated cytosines to uracil, while methylated cytosines remain unchanged.
  • the target regions containing the CpGs of interest were amplified by PCR using a specific primer pair per target region, each containing a T7-promoter-tagged reverse primer, respectively.
  • RNA transcripts were specifically cleaved at uracil residues and dispensed onto a SpectroCHIP Array. This chip was placed into a MALDI-TOF mass spectrometer for data acquisition and the resulting data was analyzed with EpiTYPER software.
  • msPCR real-time quantitative methylation specific PCR
  • a specific set of three oligonucleotides was designed, containing one forward primer and two reverse primers.
  • the two reverse primers were designed such that one is having a G at the 3′ end that is complementary to the methylated, unchanged C while the second forward primer is having an A at the 3′ end that is complementary to the converted uracil.
  • buccal cells were collected from a number of persons with buccal swabs and genomic DNA was purified from the buccal cells using a QIAamp 96 DNA Swab BioRobot Kit (Qiagen, Hilden, Germany).
  • the purified genomic DNA was treated with sodium bisulfite using the Zymo EZ DNA Methylation Kit (Zymo, Irvine, Calif., USA). This treatment converts unmethylated cytosines to uracil, while methylated cytosines remain unchanged.
  • methylation levels of CpGs contained in the sample For each set of three oligonucleotides two PCR reactions were initiated, the first PCR reaction using the forward and the first of the two reverse primers, the second PCR reaction using the forward and the second of the two reverse primers. The methylation level of each CpG was determined, using real-time quantitative msPCR with TaqMan probes specific for each amplified target region.
  • DNA methylation levels of 289 individuals (259 for the training data set and 30 for the test data set) have been determined as described in Example 1 unless noted differently.
  • the DNA methylation levels of 850000 different genomic DNA sequences have been determined from buccal swab samples using the Infinium MethylationEPIC BeadChip (IlluminaTM).
  • the methylation levels were normalized as beta values using program R v3.4.2, and thus could have a value between 0 and 1.
  • the data set i.e. the training data set, was a data matrix with a structure as in Table 1.
  • Age +53.9126* cg 27320127+43.1588* cg 16267121+31.5464* cg 00831672+30.4384* cg 27173374+26.5197* cg 16867657+20.9302* cg 14681176+19.0975* cg 25606723+16.8674* cg 11607603+16.6092* cg 08097417+15.0595* cg 11330075+14.5786* cg 12333719+14.1955* cg 10543136+13.6743* cg 21807065+12.4988* cg 19851481+12.1954* cg 08224787+11.7822* cg 19702785+11.7706* cg 13759931+11.6845* cg 19112204+11.4521* cg 07955995+10.869* cg 18815943+10.829* cg 2472
  • This age indicator comprised 148 terms such as +16.6092*cg08097417, wherein a positive sign indicated that the methylation level positively correlated with age, and a negative sign indicated that the methylation level negatively correlated with age.
  • a numbered cg refers to a genomic DNA sequence according to the Infinium MethylationEPIC BeadChip; and the absolute value of the coefficient with which the cg is multiplied indicates the importance of this cg.
  • the statistics have been determined with an independent test data set consisting of data of 30 individuals (about 10%) which were different from the 259 (289-30) individuals used for the training data set but which were drawn from the same population as said 289 individuals.
  • Example 5 Generation of an Age Predictor Using LASSO and Subsequent Stepwise Regression
  • Stepwise regression was applied on a reduced training data set obtained after performing LASSO (Example 4) to distill the best significant set of cg sites/CpGs and thereby optimize the model.
  • the reduced training data set (IME_blasso[, ⁇ 1]) was the same as the training data set used in Example 4 except that it retained only the 148 columns relating to the 148 cg sites selected by LASSO.
  • Stepwise regression was performed using the statistical software R v3.4.1 and the following command:
  • Age +66.2822* cg 11330075+65.203* cg 00831672+55.7265* cg 27320127+44.4116* cg 27173374+38.3902* cg 14681176+37.8069* cg 06161948+36.6564* cg 08224787+31.9397* cg 05396610+30.1919* cg 15609017+28.089* cg 09805798+27.9392* cg 19215678+27.8502* cg 12333719+27.226* cg 03741619+27.0323* cg 16677512+25.9599* cg 03230469+25.3932* cg 19851481+24.5374* cg 10543136+22.5525* cg 07291317+21.8666* cg 26430984+20.3621* cg 16
  • the age indicator contained only 88 genomic DNA sequences (cg sites/CpGs).
  • the small set of genomic DNA sequences comprised in the age indicator allows to use alternative, i.e. simpler, methods (see Examples 2 and 3) to determine the DNA methylation levels of individuals for whom the age is to be determined.
  • the age indicator was automatically updated with cases (probands; individuals) based on the decision if the domain boundaries of the test data were outside the domain boundaries of the training set of age indicator.
  • the domain boundaries were the minimum and maximum DNA methylation levels of each genomic DNA sequence comprised in the age indicator.
  • the minimum and maximum DNA methylation levels were found in the original training data set which has been used for determining the age indicator. These values change any time if the values of further individuals come in and replace the original min and max values for each of the CpGs. Min values will consequently diminish (if min is not yet 0) and max values will increase (if not yet 1) per CpG. In doing so the domain boundaries of the age indicator will expand to optimal values and it will be increasingly improbable that the age indicator is further updated.
  • DNA has been sampled from app. 200 individuals. These samples have all been obtained in northern Germany, but in order to have a broad database, care was taken to not exclude any individual in view of factors such as chronological age, general health state, obesity, level of physical fitness, drug consumption including drugs such as nicotine and alcohol. Therefore, the group is considered to be representative for the general population.
  • CpG methylation levels of the DNA from biological samples of app. 100 individuals have been determined using the method of Example 1, resulting in a large number of app. 850.000 (850000) CpGs for each individual.
  • the biglasso Package A Memory- and Computation-Effic Solver for LASSO Model Fitting with Big Data in R” by Yaohui Zeng and Patrick Breheny in arXiv:1701.05936v2 [statCO] 11 Mar. 2018.
  • XgBoost is a well known open-source software library which provides a gradient boosting framework for a number of languages.
  • XgBoost serves to amend coefficients used in a statistical model.
  • XGBoost A Scalable Tree Boosting System
  • XGBoost A Scalable Tree Boosting System
  • 70 CpG would constitute a useful selection of CpG from the initially considered app. 850000 different CpGs. From these 70 CpG, 10 were overlapping with only those of the first group, 12 were were overlapping with only those of the second group and 8 were overlapping with both groups.
  • a useful model can be established that despite the small number of CpGs considered allows a determination of an age with high precision and a small confidence intervall, in particular by re-iterating parameters of a statistical model established.

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Abstract

The present invention relates to the determination of ages. Specifically, the present invention relates to a method for determining an age indicator, and a method for determining the age of an individual. Said methods are based on data comprising the DNA methylation levels of a set of genomic DNA sequences. Preferably, said age indicator is determined by applying on the data a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), preferably in combination with subsequent stepwise regression. Furthermore, the invention relates to an ensemble of genomic DNA sequences and a gene set, and their uses for diagnosing the health state and/or the fitness state of an individual and identifying a molecule which affects ageing. In further aspects, the invention relates to a chip or a kit, in particular which can be used for detecting the DNA methylation levels of said ensemble of genomic DNA sequences.

Description

  • The present invention relates to the determination of ages. Specifically, the present invention relates to a method for determining an age indicator, and a method for determining the age of an individual. Said methods are based on data comprising the DNA methylation levels of a set of genomic DNA sequences. Preferably, said age indicator is determined by applying on the data a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), preferably in combination with subsequent stepwise regression. Furthermore, the invention relates to an ensemble of genomic DNA sequences and a gene set, and their uses for diagnosing the health state and/or the fitness state of an individual and identifying a molecule which affects ageing. In further aspects, the invention relates to a chip or a kit, in particular which can be used for detecting the DNA methylation levels of said ensemble of genomic DNA sequences.
    • BACKGROUND
  • When human beings grow older, their body changes in numerous ways, for example with respect to wear of teeth, joints, weakness of muscles, decrease of the mental capabilities and so forth. However, while health may generally deteriorate as a person grows old, even for persons having the same birth date, there are still large differences in health from individual to individual. Accordingly, some people age faster than others.
  • Also, it has been found in a study observing ages of twins that only about 25% of the average lifetime is determined by genetic heritage while lifestyle and environmental factors account for the remaining 75% of lifetime variation.
  • It has been found that some diseases occur more often in human beings with increasing chronological age. However, the chronological age is not the ideal indicator for the age-associated health state of an individual which is often called the “biological age”. Determination of an age which is more similar to the biological age might be helpful in assessing whether or not an individual has a higher risk for ageing-related diseases such as Alzheimer's disease. If the determined age is higher than the chronological age, preventive measures, e.g. a change in life-style, might be indicated to prevent or slow down the course of ageing-related diseases. The determination of an alternative age might be also useful for improving diagnostics, for example, evaluating, if a focus should be put on ageing-related diseases or not.
  • Furthermore, if the chronological age of an individual is not known, the alternative age—despite not being the same—could be used as an indicator of the chronological age. If the alternative age determination is based on a biological sample, it may be used, for example, also in forensics, where traces of blood from an offender are found at a crime scene.
  • It has further been proposed that certain groups of individuals age slower than others, for example, people in certain countries having specific local habits with respect to nutrition and so forth. Determination of the age of individuals of different groups may help identifying factors influencing the biological age. Reference is made to Alegria-Torres et al., Epigenomics, 2011 June; 3(3): 267-277.
  • It is noted that where both the chronological age and an age different from the chronological age are known, what could be indicated is a difference to the chronological age rather than the absolute value.
  • It has been suggested to determine the age of a human being based on the levels of methylation of genomic DNA sequences found in that individual. In particular, reference is made to WO 2012/162139. In WO 2012/162139 it has been suggested to observe cytosine methylation of one or more of CG loci in the genomic DNA selected from a large group of CG loci designations.
  • Reference is also made to WO 2015/048665 where additional CpG loci are listed.
  • It has also been suggested in document WO 2012/162139 that one could collect a reference (training) data set of, for example, 100 individuals of varying chronological ages using specific technology platforms and tissues and to then design a specific multivariate linear model that is fit to this reference data set comprising the methylation levels of CpG loci obtained for each individual. For estimating the coefficients, for example, least squares regression has been suggested. The coefficients assigned to each CpG locus would then be used to determine the unknown alternative ages of individuals not included in the training data set. It has been suggested to use a “leave-one-out analysis” in determining these coefficients. In such a “leave-one-out analysis” the multivariate regression model is fit on all but one subject of the reference data set and the prediction is then compared to the chronological age of the left-out subject. Also, tests have been suggested by WO 2012/162139 to screen for top predictors so as to improve the accuracy of the model.
  • Nonetheless, despite the use of a very large number of CpG loci and substantive experimental and computational effort deriving an age indicator from the very large number of corresponding methylation level measurement values, the average accuracy obtained by WO 2012/162139 is stated to still be only in a range of 3 to 5 years. This demonstrates, that the accuracy and/or efficiency of current age determination methods is suboptimal.
  • Furthermore, measuring and evaluating a large number of methylation levels is costly.
  • In this respect it is to be noted that about 28 Million CpG loci can be found in the human genome. Even if it is considered that methylation levels of some of these CpG loci might not be affected by aging, a very large number of CpG loci remain that have methylation levels affected by age. While it is believed that the detection methods used in determining methylation levels might improve over time, allowing to determine the methylation levels of a growing number of CpG loci, it is currently possible already to determine the methylation levels of at least app. 800.000 (800000) CpG loci using commercially available instruments and methods. Still, such measurements are expensive, and thus, the determination of an age based on measuring a very large number of CpG loci would be very expensive. Thus, current age determination methods are based on a few hundreds of CpG loci. However, the costs, equipment and expertise required for determining the age based on a few hundreds of CpG loci are still a roadblock for the wide-spread use of current age determining methods.
  • Accordingly, there is a need for improved age determination methods. In particular, there is a need for improved age determination methods which require less data input while having at least about the same accuracy.
  • There is further a need for improved means for screening drugs for treating or preventing an ageing-related disease or cancer, or a phenotype associated with an ageing-related disease, or cancer. In particular, such means are also desirable for diagnosing the health state or fitness state of an individual.
  • It is also desirable to determine an age in a cost-effective manner.
  • It would also be desirable to allow a determination of an age that even if not very cost-effective and/or not very precise at least allows an independent evaluation of other methods of age determination. In other words, there is a need for an alternative age indicator which can be used to validate the age determined with other age indicators. Such a cross-validation is very important in diagnostics.
    • SUMMARY
  • Means to address the technical problem above are provided in the claims and outlined herein below.
  • In its broadest aspect, the present invention relates to a method for determining an age indicator, a method for determining the age of an individual, and/or an ensemble of genomic DNA sequences.
  • In particular, the method for determining an age indicator of the invention and as provided herein comprises the steps of
    • (a) providing a training data set of a plurality of individuals comprising for each individual
      • (i) the DNA methylation levels of a set of genomic DNA sequences and
      • (ii) the chronological age, and
    • (b) applying on the training data set a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), thereby determining the age indicator and a reduced training data set,
      • wherein the independent variables are the methylation levels of the genomic DNA sequences and preferably wherein the dependent variable is the age,
      • wherein the age indicator comprises
        • (i) a subset of the set of genomic DNA sequences as ensemble and
        • (ii) at least one coefficient per genomic DNA sequence contained in the ensemble, and
        • wherein the reduced training data set comprises all data of the training data set except the DNA methylation levels of the genomic DNA sequences which are eliminated by the LASSO.
  • In particular, the method for determining the age of an individual comprises the steps of
    • (a) providing a training data set of a plurality of individuals comprising for each individual
      • (i) the DNA methylation levels of a set of genomic DNA sequences and
      • (ii) the chronological age, and
    • (b) applying on the training data set a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), thereby determining the age indicator and a reduced training data set,
      • wherein the independent variables are the methylation levels of the genomic DNA sequences and preferably wherein the dependent variable is the age,
      • wherein the age indicator comprises
        • (i) a subset of the set of genomic DNA sequences as ensemble and
        • (ii) at least one coefficient per genomic DNA sequence contained in the ensemble, and
        • wherein the reduced training data set comprises all data of the training data set except the DNA methylation levels of the genomic DNA sequences which are eliminated by the LASSO, and
    • (c) providing the DNA methylation levels of the individual for whom the age is to be determined of at least 80%, preferably 100% of the genomic DNA sequences comprised in the age indicator, and
    • (d) determining the age of the individual based on its DNA methylation levels and the age indicator, preferably wherein the determined age can be different from the chronological age of the individual.
  • In particular, the ensemble of genomic DNA sequences comprises least one, preferably at least 10, preferably at least 50, preferably at least 70, preferably all of cg11330075, cg25845463, cg22519947, cg21807065, cg09001642, cg18815943, cg06335143, cg01636910, cg10501210, cg03324695, cg19432688, cg22540792, cg11176990, cg00097800, cg27320127, cg09805798, cg03526652, cg09460489, cg18737844, cg07802350, cg10522765, cg12548216, cg00876345, cg15761531, cg05990274, cg05972734, cg03680898, cg16593468, cg19301963, cg12732998, cg02536625, cg24088134, cg24319133, cg03388189, cg05106770, cg08686931, cg25606723, cg07782620, cg16781885, cg14231565, cg18339380, cg25642673, cg10240079, cg19851481, cg17665505, cg13333913, cg07291317, cg12238343, cg08478427, cg07625177, cg03230469, cg13154327, cg16456442, cg26430984, cg16867657, cg24724428, cg08194377, cg10543136, cg12650870, cg00087368, cg17760405, cg21628619, cg01820962, cg16999154, cg22444338, cg00831672, cg08044253, cg08960065, cg07529089, cg11607603, cg08097417, cg07955995, cg03473532, cg06186727, cg04733826, cg20425444, cg07513002, cg14305139, cg13759931, cg14756158, cg08662753, cg13206721, cg04287203, cg18768299, cg05812299, cg04028695, cg07120630, cg17343879, cg07766948, cg08856941, cg16950671, cg01520297, cg27540719, cg24954665, cg05211227, cg06831571, cg19112204, cg12804730, cg08224787, cg13973351, cg21165089, cg05087008, cg05396610, cg23677767, cg21962791, cg04320377, cg16245716, cg21460868, cg09275691, cg19215678, cg08118942, cg16322747, cg12333719, cg23128025, cg27173374, cg02032962, cg18506897, cg05292016, cg16673857, cg04875128, cg22101188, cg07381960, cg06279276, cg22077936, cg08457029, cg20576243, cg09965557, cg03741619, cg04525002, cg15008041, cg16465695, cg16677512, cg12658720, cg27394136, cg14681176, cg07494888, cg14911690, cg06161948, cg15609017, cg10321869, cg15743533, cg19702785, cg16267121, cg13460409, cg19810954, cg06945504, cg06153788, and cg20088545, or a fragment thereof which comprises at least 70%, preferably at least 90% of the continuous nucleotide sequence.
  • Preferably, said ensemble of genomic DNA sequences is comprised in the reduced training data set and/or the age indicator obtained by said method for determining an age indicator.
  • In a further preferred aspect, the invention relates to a gene set comprising at least one, preferably at least 10, preferably at least 30, preferably at least 50, preferably at least 70, preferably all of SIM bHLH transcription factor 1 (SIM1), microtubule associated protein 4 (MAP4), protein kinase C zeta (PRKCZ), glutamate ionotropic receptor AMPA type subunit 4 (GRIA4), BCL10, immune signaling adaptor (BCL10), 5′-nucleotidase domain containing 1 (NT5DC1), suppression of tumorigenicity 7 (ST7), protein kinase C eta (PRKCH), glial cell derived neurotrophic factor (GDNF), muskelin 1 (MKLN1), exocyst complex component 6B (EXOC6B), protein S (PROS1), calcium voltage-gated channel subunit alpha1 D (CACNA1D), kelch like family member 42 (KLHL42), OTU deubiquitinase 7A (OTUD7A), death associated protein (DAP), coiled-coil domain containing 179 (CCDC179), iodothyronine deiodinase 2 (DIO2), transient receptor potential cation channel subfamily V member 3 (TRPV3), MT-RNR2 like 5 (MTRNR2L5), filamin B (FLNB), furin, paired basic amino acid cleaving enzyme (FURIN), solute carrier family 25 member 17 (SLC25A17), Gpatch domain containing 1 (GPATCH1), UDP-GlcNAc:betaGal beta-1,3-Nacetylglucosaminyltransferase 9 (B3GNT9), zyg-11 family member A, cell cycle regulator (ZYG11A), seizure related 6 homolog like (SEZ6L), myosin X (MYO10), acetyl-CoA carboxylase alpha (ACACA), G protein subunit alpha i1 (GNAI1), CUE domain containing 2 (CUEDC2), homeobox D13 (HOXD13), Kruppel like factor 14 (KLF14), solute carrier family 1 member 2 (SLC1A2), acetoacetyl-CoA synthetase (AACS), ankyrin repeat and sterile alpha motif domain containing 1A (ANKS1A), microRNA 7641-2 (MIR7641-2), collagen type V alpha 1 chain (COL5A1), arsenite methyltransferase (AS3MT), solute carrier family 26 member 5 (SLC26A5), nucleoporin 107 (NUP107), long intergenic non-protein coding RNA 1797 (LINC01797), myosin IC (MYO1C), ankyrin repeat domain 37 (ANKRD37), phosphodiesterase 4C (PDE4C), EF-hand domain containing 1 (EFHC1), uncharacterized LOC375196 (LOC375196), ELOVL fatty acid elongase 2 (ELOVL2), WAS protein family member 3 (WASF3), chromosome 17 open reading frame 82 (C17orf82), G protein-coupled receptor 158 (GPR158), F-box and leucine rich repeat protein 7 (FBXL7), ripply transcriptional repressor 3 (RIPPLY3), VPS37C subunit of ESCRT-I (VPS37C), polypeptide Nacetylgalactosaminyltransferase like 6 (GALNTL6), DENN domain containing 3 (DENND3), nuclear receptor corepressor 2 (NCOR2), endothelial PAS domain protein 1 (EPAS1), PBX homeobox 4 (PBX4), long intergenic non-protein coding RNA 1531 (LINC01531), family with sequence similarity 110 member A (FAM110A), glycosyltransferase 8 domain containing 1 (GLT8D1), G protein subunit gamma 2 (GNG2), MT-RNR2 like 3 (MTRNR2L3), zinc finger protein 140 (ZNF140), kinase suppressor of ras 1 (KSR1), protein disulfide isomerase family A member 5 (PDIA5), spermatogenesis associated 7 (SPATA7), pantothenate kinase 1 (PANK1), ubiquitin specific peptidase 4 (USP4), G protein subunit alpha q (GNAQ), potassium voltage-gated channel modifier subfamily S member 1 (KCNS1), DNA polymerase gamma 2, accessory subunit (POLG2), storkhead box 2 (STOX2), neurexin 3 (NRXN3), BMS1, ribosome biogenesis factor (BMS1), forkhead box E3 (FOXE3), NADH:ubiquinone oxidoreductase subunit A10 (NDUFA10), relaxin family peptide receptor 3 (RXFP3), GATA binding protein 2 (GATA2), isoprenoid synthase domain containing (ISPD), adenosine deaminase RNA specific B1 (ADARB1), Wnt family member 7B (WNT7B), pleckstrin and Sec7 domain containing 3 (PSD3), membrane anchored junction protein (MAJIN), pyridine nucleotide-disulphide oxidoreductase domain 1 (PYROXD1), cingulin like 1 (CGNL1), chromosome 7 open reading frame 50 (C7orf50), MORN repeat containing 1 (MORN1), atlastin GTPase 2 (ATL2), WD repeat and FYVE domain containing 2 (WDFY2), transmembrane protein 136 (TMEM136), inositol polyphosphate-5-phosphatase A (INPP5A), TBC1 domain family member 9 (TBC1D9), interferon regulatory factor 2 (IRF2), sirtuin 7 (SIRT7), collagen type XXIII alpha 1 chain (COL23A1), guanine monophosphate synthase (GMPS), potassium two pore domain channel subfamily K member 12 (KCNK12), SIN3-HDAC complex associated factor (SINHCAF), hemoglobin subunit epsilon 1 (HBE1), and tudor domain containing 1 (TDRD1).
  • Preferably, said gene set is obtained by selecting from said ensemble of genomic DNA sequences those genomic DNA sequences which encode a protein, or a microRNA or long noncoding RNA.
  • In further preferred aspects, the invention relates to the use of the ensemble of genomic DNA sequences or the gene set according to the invention for diagnosing the health state and/or the fitness state of an individual.
  • In further preferred aspects, the invention relates to an in silico and/or in vitro screening method for identifying a molecule which affects ageing comprising a step of providing the ensemble of genomic DNA sequences or the gene set according to the invention, wherein the molecule ameliorates, prevents and/or reverses at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer when administered to an individual.
  • In further preferred aspects, the invention relates to a chip or a kit, in particular which can be used for detecting the DNA methylation levels of the ensemble of genomic DNA sequences or the gene set according to the invention.
  • In particular, the chip comprises the genomic DNA sequences or the gene set according to the invention, wherein each sequence is contained in a separate spot.
  • In particular, the kit comprises
    • (a) at least one unique primer pair,
    • wherein of each primer pair one primer is a forward primer binding to the reverse strand and the other primer is a reverse primer binding to the forward strand of one the genomic DNA sequences comprised in the ensemble of genomic DNA sequences or one of the genes comprised in the gene set according to the invention,
    • and wherein the two nucleotides which are complementary to the 3′ ends of the forward and reverse primers are more than 30 and less than 3000, preferably less than 1000 nucleotides apart, or
    • (b) at least one probe which is complementary to one of the genomic DNA sequences comprised in the ensemble of genomic DNA sequences or one of the genes comprised in the gene set according to the invention.
  • The invention is, at least partly, based on the surprising discovery that an age indicator comprising a further reduced set of genomic DNA sequences, but still having an acceptable quality, could be determined by applying a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), wherein the independent variables are the methylation levels of the genomic DNA sequences and the dependent variable is the age. This was especially surprising as the ridge regression (L2 parameter), which was required in previous methods, was omitted. Further surprisingly, there was very little overlap between the set of genomic DNA sequences determined in the present invention and previously determined sets of genomic DNA sequences. It is thus further surprising that an age indicator comprising very different genomic DNA sequences than known age indicators, but also performing well, could be found.
  • Reducing the number of genomic DNA sequences while ensuring accurate age determination has many advantages. One advantage is reducing costs, efforts and/or necessary expertise for determining the DNA methylation levels of the genomic DNA sequences, in particular because it allows to use simpler laboratory methods. Another advantage is to narrow down drug target candidates which are encoded by the reduced ensemble of genomic DNA sequences. A further advantage is to provide an alternative or improved tool for diagnosing the health state of an individual. Thus, a method for determining alternative or improved age indicators is also useful for validating the results obtained by other methods, i.e. a diagnosis or drug candidates.
    • General Terms
  • Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art to which the invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, preferred methods and materials are described. For the purposes of the present invention, the following terms are defined below.
  • The articles “a” and “an” are used herein refer to one or to more than one (i.e. to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
  • As used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (or).
  • It is an object of the invention to provide novelties for the industrial application. This object is achieved by what is claimed in the independent claims.
  • Some preferred embodiments are described in the dependent claims. It will be obvious to the skilled person that preferred embodiments currently not claimed can be found in the description. Furthermore, it is noted that certain aspects of the invention despite not being claimed in independent claims for the time being may be found in the description and might be referred to later on.
    • DETAILED DESCRIPTION
  • In the following described are embodiments and definitions relating to the method for determining an age indicator according to the present invention, the age indicator obtained by said method, the ensemble of genomic DNA sequences comprised in said age indicator, and the method for determining the age of an individual according to the present invention.
  • As used herein, an age indicator refers to a statistical model which can be used for determining the age of an individual based on the DNA methylation levels of certain genomic DNA sequences of said individual.
  • The determined age of an individual, as used herein, is not necessarily the same age as the chronological age of said individual. Usually, the determined age and the chronological age of an individual are different, and it is coincidence when they are the same. The determined age is also termed “alternative age” herein. Any age may be counted in “years” and/or, preferably, in “days”. The determined age of an individual, as used herein, is a better indicator of the biological age of said individual than his chronological age. The chronological age of an individual refers to the time which has passed since birth of the individual. The biological age, as used herein, relates to the health state of an individual. Preferably, the health state relates to the state of at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer, wherein the state indicates the absence, presence, or stage of the disease or the phenotype associated with a disease. Thus, the age indicator of the invention can be used for diagnosing the health state of an individual.
  • In particular, the age indicator, as used herein, refers to a linear model which comprises independent variables. Herein, an independent variable comprised in the age indicator or a linear model used for generating the age indicator refers to the DNA methylation level of a certain genomic DNA sequence.
  • Preferably, the dependent variable of the age indicator of the invention and/or the linear model used for generating the age indicator of the invention is the age.
  • In the linear model, the age of a plurality of individuals is predicted by a set of independent variables (the methylation levels of certain genomic DNA sequences), wherein each independent variable has at least one coefficient. The predicted age and the chronological age preferably correlate very well or, in other words, are preferably in average very similar. However, the predicted age, also termed herein the “determined age”, of one individual, may differ, for example for several years, from his chronological age.
  • Specifically, the methylation level, as used herein, refers to the beta value. The beta value, as used herein, describes the ratio of methylated cytosines over the sum of methylated and unmethylated cytosines among all relevant cytosines within a certain part of the genomic DNA of all alleles of all cells contained in a sample. The methylation state of one particular cytosine molecule is binary and is either unmethylated (0; 0%) or methylated (1; 100%). A methylated cytosine is also termed “5′mC”. In consequence, the beta value for a cytosine at a particular position in the genomic DNA of a single cell having two alleles is thus usually either 0, 0.5 or 1. Thus, the beta value at a particular CpG position in the genomic DNA of a population of cells (regardless of the allele number) can take a value between 0 and 1. Furthermore, the beta value when considering all CpGs within a certain genomic DNA sequence of a single allele can take a value between 0 and 1. Preferably herein, only one CpG is considered within a certain genomic DNA sequence. Herein, the sample comprises preferably more than one cell which might comprise more than one allele. Thus, it is evident that the beta value of a genomic DNA sequence, as used herein, can virtually take any value between 0 and 1. Herein, the methylation level of a CpG is defined by the cytosine, and not the guanine, comprised in said CpG.
  • Preferably herein, CGs/CpGs correspond to Illumina™ probes specified by so called Cluster CG numbers (Illumina™ methylation probe ID numbers). The methylation levels of a preselected set of CpGs can be measured using an Illumina™ DNA methylation array. To quantify the methylation level of a CpG, one can use software to calculate the beta value of methylation. An Illumina™ methylation probe ID is characterized by the term “cg” followed by a number, for example cg11330075 or cg25845463. The terms “CG”, “cg”, “CpG”, “CpG locus”, “CpG site”, and “cg site” are used interchangeably herein. Determination of DNA methylation levels with Illumina™ DNA methylation array is well known, established and can be used in the present invention, although other methods will be described and might be preferred for reasons indicated. Thus, alternatively or in addition, methylation levels of CpGs can be quantified using other methods known in the art as well. Nonetheless, unless indicated otherwise, the CGs/CpGs identified in the present invention correspond to the Illumina™ methylation probe IDs.
  • Furthermore, although possible, it is not required for determining the methylation level of a genomic DNA sequence to determine the methylation of cytosines at a single-nucleotide resolution, but the average methylation signal of relevant cytosines within said sequence is sufficient. Preferably, only cytosines which are followed by a guanine (CpG dinucleotides) are considered relevant herein. The common names for bases and nucleotides, e.g. cytosine and cytidine, respectively, are used interchangeably herein and refer to a specific nucleotide comprising the respective base. Herein, the terms “methylation level” and “DNA methylation level” are used interchangeably. The ranges of 0% to 100% and 0 to 1 are used interchangeably herein when referring to methylation levels.
  • As used herein, a genomic DNA sequence refers to a coherent part of the genomic DNA of an individual. Herein, a certain genomic DNA sequence does not have to be necessarily identical to the reference sequence of the genomic DNA sequence it relates to, but it may be a variant thereof. Preferably, the genomic DNA sequence is a unique sequence. A skilled person can easily determine if a sequence is a variant of a certain reference genomic DNA sequence by interrogating databases such as “GenBank” or “EMBL-NAR” and using general knowledge.
  • Herein, the methylation level of a genomic DNA sequence refers to the methylation level of at least one cytosine within at least one CpG dinucleotide comprised in said genomic DNA sequence.
  • Preferably herein, the methylation level of a genomic DNA sequence refers to the methylation level of exactly one cytosine within exactly one CpG dinucleotide comprised in said genomic DNA sequence. Preferably, said genomic DNA sequence comprises further nucleotides whereof the methylation levels are not considered, but which allow identification of said CpG dinucleotide. Thus herein, a genomic DNA sequence may be defined by a CpG locus.
  • Very preferably herein, a genomic DNA sequence is defined by an Illumina™ methylation probe ID. The terms “Illumina™ methylation probe ID”, “Illumina™ CpG cluster ID”, “Illumina™ Cluster CG number”, “Illumina™ probe”, Illumina™ methylation probe ID number, with or without the terms “Illumina™” or “™”, and equivalents thereof, are used interchangeably herein.
  • A plurality of individuals, as used herein, refers to more than one individual. An individual, as used herein, refers to a living being which has 5′-methylated cytosines (5′-mc) within its genomic DNA. Preferably a living being is a vertebrate, more preferably a mammal, most preferably a human. Preferably, the methylation level of at least one genomic DNA sequence of the individual is associable with ageing and/or the health state of the individual. As used herein, an individual can have any sex, for example, it may be a male, a female, a hermaphrodite or others. Thus, the terms “he”, “she”, “it”, or “his”, “her”, “its” are used interchangeably herein in the context of an individual.
  • Usually, the identity of an individual is known, but this is not required. In particular, the age of an individual can be determined by the method of the invention even if the identity and/or the chronological age of the individual is unknown. Thus, the method for determining the age of an individual according to the present invention allows to predict the chronological age of an individual whereof only a biological sample is available. Such a biological sample comprises, for example, hair cells, buccal cells, saliva, blood and/or sperm. Thus, the method for determining the age of an individual is useful for estimating the chronological age of an individual who was present at a crime scene and has left some of his/her biological material there. Furthermore, the method for determining the age of an individual is useful for estimating the chronological age of an individual when no data about the chronological age of said individual have been recorded or are available.
  • A regression method, as used herein, refers to a statistical process for estimating the relationships among variables, in particular the relationship between a dependent variable and one or more independent variables. Regression analysis is also used to understand which among the independent variables are related to the dependent variable, and to explore the forms of these relationships. Preferably, the regression method comprises a linear regression. Preferably, the regression method comprises a linear regression that uses shrinkage. Shrinkage is where data values are shrunk towards a central point, like the mean. Herein, the regression method comprises a Least Absolute Shrinkage and Selection Operator (LASSO).
  • LASSO encourages simple, sparse models (i.e. models with fewer parameters). This particular type of regression is well-suited for models showing high levels of multicollinearity or when automation of certain parts of the model selection is desired, like variable selection and/or parameter elimination. LASSO regression performs L1 regularization, which adds a penalty equal to the absolute value of the magnitude of coefficients. This type of regularization can result in sparse models with few coefficients; some coefficients can become zero and eliminated from the model. Larger penalties result in coefficient values closer to zero, which is the ideal for producing simpler models. In other words, LASSO can be used for reducing the number of independent variables of a linear model. The terms “LASSO”, “lasso” and “Lasso regression” are used synonymously herein.
  • In preferred embodiments, the LASSO is performed with the biglasso R package, preferably by applying the command “cv.biglasso”. Preferably, the “nfold” is 20.
  • In preferred embodiments, the LASSO L1 regularization parameter/alpha parameter is 1.
  • Preferably, the regression method of the invention does not comprise a Ridge regression (L2 regularization) or the L2 regularization parameter/lambda parameter is 0.
  • In contrast, in the Elastic Net method, the L1 regularization parameter or alpha parameter is not 1, but around 0.1 to 0.9. Furthermore, the Elastic Net method comprises a Ridge regression. Thus, preferably, the regression method of the invention does not comprise an Elastic Net method. Furthermore, the age indicator of the invention is preferably not determined by applying an Elastic Net method.
  • Preferably, the regression method of the invention further comprises applying a stepwise regression subsequently to the LASSO. Preferably, the stepwise regression is applied on the reduced training data set.
  • Thus, in particularly preferred embodiments, the method for determining an age indicator comprises the steps of
    • (a) providing a training data set of a plurality of individuals comprising for each individual
      • (i) the DNA methylation levels of a set of genomic DNA sequences and
      • (ii) the chronological age, and
    • (b) applying on the training data set a regression method comprising
      • (i) a Least Absolute Shrinkage and Selection Operator (LASSO), thereby determining a reduced training data set, and
      • (ii) subsequent stepwise regression, thereby determining the age indicator, preferably
      • wherein said stepwise regression is applied on said reduced training data set,
      • wherein the independent variables are the methylation levels of the genomic DNA sequences and preferably wherein the dependent variable is the age,
      • wherein the age indicator comprises
        • (i) a subset of the set of genomic DNA sequences as ensemble and
        • (ii) at least one coefficient per genomic DNA sequence contained in the ensemble, and
      • wherein the reduced training data set comprises all data of the training data set except the DNA methylation levels of the genomic DNA sequences which are eliminated by the LASSO.
  • Thus, in particularly preferred embodiments, the method for determining the age of an individual comprises the steps of
    • (a) providing a training data set of a plurality of individuals comprising for each individual
      • (i) the DNA methylation levels of a set of genomic DNA sequences and
      • (ii) the chronological age, and
    • (b) applying on the training data set a regression method comprising
      • (i) a Least Absolute Shrinkage and Selection Operator (LASSO), thereby determining a reduced training data set, and
      • (ii) subsequent stepwise regression, thereby determining the age indicator, preferably
      • wherein said stepwise regression is applied on said reduced training data set,
      • wherein the independent variables are the methylation levels of the genomic DNA sequences and preferably wherein the dependent variable is the age,
      • wherein the age indicator comprises
        • (i) a subset of the set of genomic DNA sequences as ensemble and
        • (ii) at least one coefficient per genomic DNA sequence contained in the ensemble, and
      • wherein the reduced training data set comprises all data of the training data set except the DNA methylation levels of the genomic DNA sequences which are eliminated by the LASSO, and
    • (c) providing the DNA methylation levels of the individual for whom the age is to be determined of at least 80%, preferably 100% of the genomic DNA sequences comprised in the age indicator, and
    • (d) determining the age of the individual based on its DNA methylation levels and the age indicator, preferably wherein the determined age can be different from the chronological age of the individual.
  • Stepwise regression, as used herein, is a method of fitting regression models in which the choice of predictive variables is carried out by an automatic procedure. In each step, a variable is considered for addition to or subtraction from the set of explanatory variables based on some prespecified criterion. This may take the form of a sequence of F-tests or t-tests, but other techniques are possible, such as adjusted R2, Akaike information criterion (AIC), Bayesian information criterion, Mallows's Cp, PRESS, or false discovery rate. The main approaches are forward selection, backward elimination and bidirectional elimination. Forward selection involves testing the addition of each variable using a chosen model fit criterion, adding the variable (if any) whose inclusion gives the most statistically significant improvement of the fit, and repeating this process until none improves the model to a statistically significant extent.
  • Backward elimination involves testing the deletion of each variable using a chosen model fit criterion, deleting the variable (if any) whose loss gives the most statistically insignificant deterioration of the model fit, and repeating this process until no further variables can be deleted without a statistically significant loss of fit. Bidirectional elimination is a combination of forward selection and backward elimination, testing at each step for variables to be included or excluded. Preferably herein, the variables considered by the stepwise regression are the variables which are selected by the LASSO regression.
  • In a preferred embodiment, the stepwise regression is a bidirectional elimination. Preferably, statistically insignificant independent variables are removed when applying said stepwise regression. Preferably, the significance level for determining if a variable is added/included or removed/excluded is 0.05.
  • For determining an age indicator according to the invention, a set of genomic DNA sequences is reduced by the regression method according to the invention in at least one step, preferably in two steps. Preferably, the starting set of genomic DNA sequences is preselected from genomic DNA sequences whereof the methylation level is associable with chronological age. Such a preselected set is, for example, an Illumina™ DNA methylation array. Then, the LASSO is applied thereby determining an age indicator and a reduced training data set, which both comprise an ensemble of genomic DNA sequences.
  • In certain embodiments, the set of genomic DNA sequences comprised in the training data set is preselected from genomic DNA sequences whereof the methylation level is associable with chronological age. Preferably, the preselected set comprises at least 400000, preferably at least 800000 genomic DNA sequences. Particularly suitable are sequences assayed by the Infinium MethylationEPIC BeadChip Kit.
  • In certain embodiments, the genomic DNA sequences comprised in the training data set are not overlapping with each other and/or only occur once per allele. This is particularly preferred, when only a comparably small set of genomic DNA sequence is preselected, i.e. less than 10000.
  • In a preferred embodiment, the stepwise regression is applied on the reduced training data set, thereby determining an age indicator comprising an ensemble of genomic DNA sequences.
  • It has been further surprisingly found that the ensemble of genomic DNA sequences determined by applying LASSO and subsequent stepwise regression is smaller and the respective age indicator has a better performance than the ensemble of genomic DNA sequences or the age indicator determined by applying only LASSO without stepwise regression.
  • It was further surprisingly found that, although having less variables, an age indicator determined by applying LASSO and subsequent stepwise regression had an accuracy which was at least about as high or even improved compared to prior art methods such as in Horvath, Genome Biology 2013, 14:R115.
  • Herein, the subset comprised in the age indicator is also termed “ensemble” or “ensemble of genomic DNA sequences”. As used herein, the subset of genomic DNA sequences (ensemble) is maximally as big as the set of genomic DNA sequences.
  • Preferably, the ensemble comprised in the age indicator of the invention is smaller than the set of genomic DNA sequences used for determining said age indicator.
  • Preferably, the ensemble comprised in the age indicator of the invention is smaller than the set of genomic DNA sequences comprised in the reduced training data set used for determining said age indicator.
  • In certain embodiments, the reduced training data set comprises at least 90, preferably at least 100, preferably at least 140 genomic DNA sequences.
  • In certain embodiments, the reduced training data set comprises less than 5000, preferably less than 2000, preferably less than 500, preferably less than 350, preferably less than 300 genomic DNA sequences.
  • The set of genomic DNA sequences comprised in the reduced training data set is preferably much reduced compared to the preselected set of genomic DNA sequences, preferably more than 90%, preferably more than 99%, preferably more than 99.9%. However, said set of genomic DNA sequences must be large enough to not prematurely limit the optimization potential of subsequent stepwise regression and/or to not obtain an age indicator with a weak performance. Herein, it is contemplated that an age indicator comprising less than 30 genomic DNA sequences has a rather weak performance compared to an age indicator comprising at least 30, preferably at least 50, preferably at least 60, preferably at least 80 genomic DNA sequences. However, an age indicator comprising as few genomic DNA sequences as possible, is preferred.
  • Thus, in certain embodiments, the age indicator comprises at least 30, preferably at least 50, preferably at least 60, preferably at least 80 genomic DNA sequences.
  • In preferred embodiments, the age indicator comprises less than 300, preferably less than 150, preferably less than 110, preferably less than 100, preferably less than 90 genomic DNA sequences.
  • In very preferred embodiments, the age indicator comprises 80 to 100, preferably 80 to 90, preferably 88 genomic DNA sequences.
  • Furthermore, the age indicator of the invention comprises at least one coefficient per genomic DNA sequence contained in the ensemble. Since one coefficient is sufficient, the age indicator preferably comprises exactly one coefficient per genomic DNA sequence contained in the ensemble.
  • A coefficient, as used herein, refers to the weight of an independent variable, which herein is the methylation level of a certain genomic DNA sequence. For predicting or determining the age of an individual, the coefficient is multiplied with the methylation level of the genomic DNA sequence or, in other words, a weight is put on each genomic DNA sequence and its methylation level; and then all weighted methylation levels are summed up. Preferably, the methylation level is between 0 and 1 (unmethylated and fully methylated, respectively).
  • Herein, the data set which is used for generating an age indicator is also called the “training data set”. As used herein, a reduced training data set refers to a training data set whereof the data of certain genomic DNA sequences are eliminated or not considered. Herein, a reduced training data set is determined by applying a regression method comprising LASSO on a training data set.
  • In preferred embodiments, the training data set comprises a matrix comprising as columns the methylation levels of the genomic DNA sequences comprised in the set of genomic DNA sequences and as rows the plurality of individuals. Preferably, the chronological age of said individuals is comprised in a further column of the matrix.
  • In certain embodiments, the age indicator of the invention is iteratively updated comprising adding the data of at least one further individual to the training data in each iteration, thereby iteratively expanding the training data set.
  • It is expected that said iterative updating of the age indicator iteratively improves the performance of the age indicator, in particular its accuracy.
  • Herein, iterative updating refers to consecutive rounds of updating the age indicator. As used herein, one round of updating or updating round is specified in certain or preferred embodiments of the invention. As used herein, different rounds of updating may refer to the same or different embodiments. Preferably, each updating round of the iteration is specified by the same embodiments of the invention. A further individual, with regard to updating the age indicator, refers to an individual which has not contributed data to the training data set, but his data are added in an updating round. Expanding the training data set, as used herein, refers to adding the data of at least one further individual to the training data set.
  • In certain embodiments, in one updating round the added data of each further individual comprise the individual's DNA methylation levels of
    • (i) at least 5%, preferably 50%, more preferably 100% of the set of genomic DNA sequences comprised in the initial or any of the expanded training data sets, and/or
    • (ii) the genomic DNA sequences contained in the reduced training data set.
  • Said option (i) refers in particular to the starting set of genomic DNA sequences, in particular to the preselected set of genomic DNA sequences. Typically, this starting set of genomic DNA sequences is large and comprises, for example, at least 800000 genomic DNA sequences. Thus, adding the methylation levels of at least 5% of the starting set to the training data set, provides a sufficiently large training data set which can be used for determining an age indicator. Preferably, the training data set is restricted to the genomic DNA sequences whereof the DNA methylation levels of all individuals comprised therein are present.
  • Thus, in preferred embodiments, all genomic DNA sequences (independent variables) which are not present for all individuals who contribute data to the expanded training data set are removed from the expanded training data set. Preferably, updating the age indicator according to said option (i) comprises adding at least 50%, preferably 100% of the set of genomic DNA sequences comprised in the initial or any of the expanded training data sets, in particular if several or many updating rounds are done.
  • In preferred embodiments, in one updating round the set of genomic DNA sequences whereof the methylation levels are added is identical for each of the further individual(s). This is particularly useful to avoid excessive removal of genomic DNA sequences within one round of updating.
  • Herein, updating of the age indicator can change the ensemble of genomic DNA sequences (independent variables) comprised therein and/or the coefficient(s) of each said genomic DNA sequence. Of note, said option (i) allows to extend, restrict and/or alter said ensemble of genomic DNA sequences, whereas option (ii) only allows to restrict said ensemble of genomic DNA sequences. Both, options (i) and (ii) allow said coefficients to change. An advantage of option (ii) however is, that only the methylation levels of a reduced set of genomic DNA sequences of the at least one further individual must be provided. Furthermore, said option (ii) is particularly useful for further reducing the size of said ensemble of genomic DNA sequences. In other words, option (i) is particularly useful for generating different age indicators for different purposes, for example, age indicators for certain groups of individuals, or to determine different age indicators as a basis for further refinements; option (ii) is particularly useful for fine-tuning and optimizing a generally already useful age indicator, i.e. for further reducing the number of independent variables, for example for its non-personalized off-the-shelf use. Both options (i) and (ii) can be combined to combine the flexibility of option (i), and the streamlining of option (ii).
  • In certain embodiments, one updating round comprises applying the LASSO on the expanded training data set, thereby determining an updated age indicator and/or an updated reduced training data set.
  • In certain embodiments, the training data set to which the data of the at least one further individual are added is the reduced training data set, which can be the initial or any of the updated reduced training data sets. Preferably, the reduced training data set is the previous reduced training data set in the iteration.
  • Thus, an updated reduced training data set can result from applying the LASSO on an expanded training data set and/or from adding data of at least one further individual to a reduced training data set.
  • In preferred embodiments, one updating round comprises applying the stepwise regression on the reduced training data set thereby determining an updated age indicator.
  • In certain embodiments, in one updating round, the data of at least one individual is removed from the training data set and/or the reduced training data set.
  • In certain embodiments, the training data set, reduced training data set and/or added data, further comprise at least one factor relating to a life-style or risk pattern associable with the individual(s) and/or a characteristic of the individual(s). Preferably, the factor is selected from drug consumption, environmental pollutants, shift work and stress.
  • In certain embodiments, the preselection of genomic DNA sequences, and/or the addition and/or removal of the data of an individual depends on at least one characteristic of the individual. Herein, the characteristic of an individual, is for example, the ethnos, the sex, the chronological age, the domicile, the birth place, at least one disease and/or at least one life style factor. As used herein, a life style factor is selected from drug consumption, exposure to an environmental pollutant, shift work or stress.
  • In certain embodiments, the training data set and/or the reduced training data set is restricted to genomic DNA sequences whereof the DNA methylation level and/or the activity/level of an encoded protein is associated with at least one of said characteristics and/or life-style factors.
  • Selecting the data in the training data set and/or the reduced training data set at any step, i.e. at the start during preselecting genomic DNA sequences and/or during updating said data sets and/or the age indicator, based on life-style factors and/or characteristics of the individuals, allows to determine age indicators which are particularly well suited for determining the age of an individual or a certain group of individuals having a certain combination of said characteristics and/or life-style factors. Furthermore, the application of different age indicators for age determination may be useful for determining certain predispositions of an individual or a group of individuals, for example, a predominant effect of stress or drug consumption. For example, if the determined age of an individual is much higher than expected when using an age indicator which has been optimized for smoking-related ageing than when using an age indicator which has been optimized for shift work related ageing, this may indicate that smoking is a more important factor for the ageing related health state of the individual than the shift work.
  • In certain embodiments, the quality of the age indicator is determined, wherein the determination of said quality comprises the steps of
    • (a) providing a test data set of a plurality of individuals who have not contributed data to the training data set comprising for each said individual
      • (i) the DNA methylation levels of the set of genomic DNA sequences comprised in the age indicator and
      • (ii) the chronological age; and
    • (b) determining the quality of the age indicator by statistical evaluation and/or evaluation of the domain boundaries,
    • wherein the statistical evaluation comprises
      • (i) determining the age of the individuals comprised in the test data set,
      • (ii) correlating the determined age and the chronological age of said individual(s) and determining at least one statistical parameter describing this correlation, and
      • (iii) judging if the statistical parameter(s) indicate(s) an acceptable quality of the age indicator or not, preferably wherein the statistical parameter is selected from a coefficient of determination (R2) and a mean absolute error (MAE), wherein a R2 of greater than 0.50, preferably greater than 0.70, preferably greater than 0.90, preferably greater than 0.98 and/or a MAE of less than 6 years, preferably less than 4 years, preferably at most 1 year, indicates an acceptable quality, and
    • wherein evaluation of the domain boundaries comprises
      • (iv) determining the domain boundaries of the age indicator,
      • wherein the domain boundaries are the minimum and maximum DNA methylation levels of each genomic DNA sequence comprised in the age indicator and
      • wherein said minimum and maximum DNA methylation levels are found in the training data set which has been used for determining the age indicator, and
      • (v) determining if the test data set exceeds the domain boundaries, wherein not exceeding the domain boundaries indicates an acceptable quality.
  • As used herein, a test data set is a data set which can be used for evaluating an age indicator that has been determined based on a training data set. Usually, said training data set and test data set have the same structure. In particular, the test data set and the training data set comprise the same set of genomic DNA sequences. As essential difference however, the test data set only contains data of individuals who have not contributed data to the respective training data set.
  • Evaluation of an age indicator, as used herein, comprises statistical evaluation and/or evaluation of the domain boundaries.
  • For the statistical evaluation, the age of the individuals of the test data set is determined and compared to the chronological age of said individuals. Any statistical measurement or parameter which is commonly used to describe the correlation of two variables can be applied. Preferably, the statistical parameter is selected from a coefficient of determination (R2) and a mean absolute error (MAE). Preferably, a R2 of greater than 0.50, preferably greater than 0.70, preferably greater than 0.90, preferably greater than 0.98 and/or a MAE of less than 6 years, preferably less than 4 years, preferably at most 1 year, indicates an acceptable quality. If not specified herein, a skilled person can evaluate the result of the measurement or the parameter based on common knowledge. In case of doubt, the quality should be judged as not acceptable.
  • If the test data set is not fully contained within the boundaries of the domain of an age indicator, the age indicator is judged to not have an acceptable quality. The domain boundaries of an age indicator, as used herein, refer to the minimum and maximum DNA methylation levels of each genomic DNA sequence comprised in the age indicator. More specifically, said minimum and maximum DNA methylation levels are found in the training data set which has been used for determining the age indicator.
  • The test data set should have a reasonable size. In particular for the statistical evaluation, it should not be too small, but comprise at least 10, preferably at least 30 individuals, preferably at least 200 individuals. For determination of the domain boundaries, the test data set should additionally not be too large, and thus comprise at most 1000 individuals, preferably at most 200 individuals. If it is larger, some violations of the domain boundaries may be allowable, for example for 5%, preferably for 1% of the individuals of the test data set.
  • In certain embodiments, the training data set and/or the test data set comprises at least 10, preferably at least 30 individuals, preferably at least 200 individuals. Preferably, the training data set comprises at least 200 individuals and the test data set comprises at least 30 individuals.
  • Of note, an age indicator which has been judged to not have an acceptable quality, can still be useful for the determination of the age on an individual. The term “acceptable quality”, as used herein, refers to the determination of an optimal age indicator, in particular through updating. Thus, an acceptable or unacceptable quality of an age indicator, as used herein, does not relate to the absolute quality of the age indicator, but to its relative quality compared to other age indicators, in particular to age indicators determined in different rounds of updating according to the method of the invention.
  • In preferred embodiments, the age indicator is updated when its quality is not acceptable. The quality is judged to be acceptable or not acceptable as explained above in the context of evaluation of the age indicator.
  • In certain embodiments, the age indicator is not further updated when the number of individuals comprised in the data has reached a predetermined value and/or a predetermined time has elapsed since a previous update. The predetermined time may also refer to the number of quality evaluations for potential updating rounds.
  • For example, if an age indicator comprises already data of many thousands or even millions of individuals, or the last 10 or even 100 evaluations with new test data sets have indicated an acceptable quality, further optimization of the age indicator is not to be expected and the updating may stop.
  • In certain embodiments, the DNA methylation levels of the genomic DNA sequences of an individual are measured in a sample of biological material of said individual comprising said genomic DNA sequences. Preferably, the sample comprises buccal cells.
  • Suitable methods for determining DNA methylation levels are, for example, methylation sequencing, bisulfate sequencing, a PCR method, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), methylation-sensitive single-strand conformation analysis, methyl-sensitive cut counting (MSCC), base-specific cleavage/MALDI-TOF, combined bisulfate restriction analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), micro array-based methods, bead array-based methods, pyrosequencing and/or direct sequencing without bisulfate treatment (nanopore technology).
  • In preferred embodiments, the DNA methylation levels of an individual are measured with a DNA methylation array such as an Illumina™ DNA methylation array, preferably an Infinium MethylationEPIC BeadChip Kit. A DNA methylation array is particularly suitable when the DNA methylation levels of a very large number of genomic DNA sequences are to be measured, in particular for starting and/or preselected genomic DNA sequences.
  • In preferred embodiments, the DNA methylation levels of genomic DNA sequences of an individual are measured by base-specific cleavage/MALDI-TOF and/or a PCR method, preferably wherein base-specific cleavage/MALDI-TOF is the Agena technology and the PCR method is methylation specific PCR. Base-specific cleavage/MALDI-TOF and/or a PCR method is particularly suitable when DNA methylation levels of a reduced set of genomic DNA sequences is to be measured, in particular for adding data to the reduced training data set and/or providing the methylation levels of an individual for whom the age is to be determined with the age indicator of the invention.
  • Further details on the determination of DNA methylation levels are explained further below in further aspects of the invention and in the Examples.
  • In certain embodiments, the method for determining an age indicator and/or the method for determining the age of an individual according to the present invention further comprise a step of obtaining a sample of biological material of an individual. The biological material may be derived from any part of the individual, but preferably the sample is obtained noninvasively. Preferably, the individual is not an embryo.
  • In a preferred embodiment, the sample is obtained from a buccal swab.
  • Herein, the age indicator of the invention can be used as a tool for determining the age of an individual. Thus, the method for determining the age of an individual according to the invention comprises all steps of the method of the invention for determining an age indicator or comprises a step of providing an age indicator according to the invention. Further, said method of determining the age of an individual comprises the steps of providing the DNA methylation levels of the individual for whom the age is to be determined of at least 80%, preferably 100% of the genomic DNA sequences comprised in said age indicator and determining the age of the individual based on its DNA methylation levels and said age indicator.
  • In other words, the methylation levels of at least 80%, preferably 100%, of the genomic DNA sequences comprised in the provided age indicator must be provided for an individual for whom the age is to be determined. The methylation levels of the genomic DNA sequences of said individual which are missing can be imputed, for example by using the median or mean of the provided methylation levels.
  • In certain embodiments, the age of the individual is determined based on its DNA methylation levels and the updated age indicator. In particular, the age is determined on the updated age indicator when the quality of the initially provided age indicator is not acceptable.
  • In preferred embodiments, the age of the individual is only determined with the age indicator when he/she has not contributed data to the training data set which is or has been used for generating said age indicator.
  • In certain embodiments, the method for determining the age of an individual further comprises a step of determining at least one life-style factor which is associated with the difference between the determined and the chronological age of said individual.
  • In preferred embodiments, the ensemble of genomic DNA sequences according to the invention does not comprise cg27320127.
  • In certain embodiments, the ensemble of genomic DNA sequences according to the invention comprises at least one, preferably at least 4, preferably at least 10, preferably at least 30, preferably at least 70, preferably all of cg11330075, cg00831672, cg27320127, cg27173374, cg14681176, cg06161948, cg08224787, cg05396610, cg15609017, cg09805798, cg19215678, cg12333719, cg03741619, cg16677512, cg03230469, cg19851481, cg10543136, cg07291317, cg26430984, cg16950671, cg16867657, cg22077936, cg08044253, cg12548216, cg05211227, cg13759931, cg08686931, cg07955995, cg07529089, cg01520297, cg00087368, cg05087008, cg24724428, cg19112204, cg04525002, cg08856941, cg16465695, cg08097417, cg21628619, cg09460489, cg13460409, cg25642673, cg19702785, cg18506897, cg21165089, cg27540719, cg21807065, cg18815943, cg23677767, cg07802350, cg11176990, cg10321869, cg17343879, cg08662753, cg14911690, cg12804730, cg16322747, cg14231565, cg10501210, cg09275691, cg15008041, cg05812299, cg24319133, cg12658720, cg20576243, cg03473532, cg07381960, cg05106770, cg04320377, cg19432688, cg22519947, cg06831571, cg08194377, cg01636910, cg14305139, cg04028695, cg15743533, cg03680898, cg20088545, cg13333913, cg19301963, cg13973351, cg16781885, cg04287203, cg27394136, cg10240079, cg02536625, and cg23128025, or a fragment thereof which comprises at least 70%, preferably at least 90% of the continuous nucleotide sequence.
  • Preferably, said ensemble of genomic DNA sequences is comprised in the age indicator obtained by the method for determining an age indicator, wherein said method comprises applying a stepwise regression subsequently to the LASSO.
  • Herein, a gene refers to a genomic DNA sequence which encodes a protein (coding sequence; CDS), or a microRNA or long non-coding RNA. Herein, a genomic DNA sequence which encodes a protein also encodes the mRNA for the translation of said protein. A microRNA (miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) that functions in RNA silencing and post-transcriptional regulation of gene expression. Long noncoding RNAs (long ncRNAs, lncRNA) are a type of transcripts with typically more than 200 nucleotides which are not translated into proteins (but possibly into peptides). Still, the majority of long non-coding RNAs are likely to be functional, i.e. in transcriptional regulation.
  • In preferred embodiments, the gene set of the invention does not comprise KCNK12.
  • In certain embodiments, the gene set of the invention comprises at least one, preferably at least 5, preferably at least 10, preferably at least 30, preferably all of ISPD, KCNK12, GNG2, SIRT7, GPATCH1, GRIA4, LINC01531, LOC101927577, NCOR2, WASF3, TRPV3, ACACA, GDNF, EFHC1, MYO10, COL23A1, TDRD1, ELOVL2, GNAI1, MAP4, CCDC179, KLF14, ST7, INPP5A, SIM1, SLC1A2, AS3MT, KSR1, DSCR6, IRF2, KCNS1, NRXN3, C11orf85, HBE1, FOXES, TMEM136, HOXD13, LOC375196, PANK1, MIR107, COL5A1, PBX4, ZNF140, GALNTL6, NUP107, LOC100507250, MTRNR2L5, C17orf82, MKLN1, FURIN, KLHL42, MORN1, ANKS1A, BCL10, DENND3, FAM110A, PROS1, WNT7B, FBXL7, GATA2, VPS37C, NRP1, POLG2, ANKRD37, GMPS, and WDFY2.
  • Preferably, said gene set is obtained by selecting from the ensemble of genomic DNA sequences those which encode a protein, or a microRNA or long non-coding RNA, wherein said ensemble of genomic DNA sequences is comprised in the age indicator obtained by the method for determining an age indicator, wherein said method comprises applying a stepwise regression subsequently to the LASSO.
  • In preferred embodiments, the ensemble of genomic DNA sequences according to the invention comprises at least one, preferably at least 4, preferably at least 10, preferably all of cg11330075, cg00831672, cg27320127, cg27173374, cg14681176, cg06161948, cg08224787, cg05396610, cg15609017, cg09805798, cg19215678, cg12333719, cg03741619, cg03230469, cg19851481, cg10543136, cg07291317, cg26430984, cg16950671, cg16867657, cg13973351, cg16781885, cg04287203, cg27394136, cg10240079, cg02536625, and cg23128025.
  • Preferably, said ensemble of genomic DNA sequences is comprised in the age indicator obtained by the method for determining an age indicator, wherein said method comprises applying a stepwise regression subsequently to the LASSO, and wherein each coefficient of said genomic DNA sequences comprised in said age indicator has an absolute value of more than 20.
  • In very preferred embodiments, the ensemble of genomic DNA sequences according to the invention comprises at least one, preferably at least 4, preferably all of cg11330075, cg00831672, cg27320127, cg10240079, cg02536625, and cg23128025.
  • Preferably, said ensemble of genomic DNA sequences is comprised in the age indicator obtained by the method for determining an age indicator, wherein said method comprises applying a stepwise regression subsequently to the LASSO, and wherein each coefficient of said genomic DNA sequences comprised in said age indicator has an absolute value of more than 40.
  • In preferred embodiments, the genomic DNA sequences comprised in the ensemble of genomic DNA sequences according to the invention, are the full sequences and not the fragments thereof.
  • In preferred embodiments, the ensemble of genomic DNA sequences according to the invention comprises the complementary sequences thereof in addition and/or in place of said ensemble of genomic DNA sequences. Herein, a genomic DNA sequence refers to the sequence as described and/or the reverse complementary sequence thereof. The skilled person can easily judge if the sequence as described or the reverse complementary sequence thereof should be used. By default, and for most applications, the sequence as described is to be used, but for some applications, for example, for determining the methylation level of said sequence with a probe, the complementary sequence thereof is used for the probe.
  • In preferred embodiments, the gene set of the invention comprises at least one, preferably at least 5, preferably at least 10, preferably at least 20, preferably all of:
  • microtubule associated protein 4 (MAP4), protein kinase C zeta (PRKCZ), glutamate ionotropic receptor AMPA type subunit 4 (GRIA4), suppression of tumorigenicity 7 (ST7), protein kinase C eta (PRKCH), calcium voltage-gated channel subunit alpha1 D (CACNA1D), death associated protein (DAP), transient receptor potential cation channel subfamily V member 3 (TRPV3), furin, paired basic amino acid cleaving enzyme (FURIN), acetyl-CoA carboxylase alpha (ACACA), G protein subunit alpha i1 (GNAI1), solute carrier family 1 member 2 (SLC1A2), phosphodiesterase 4C (PDE4C), ELOVL fatty acid elongase 2 (ELOVL2), nuclear receptor corepressor 2 (NCOR2), endothelial PAS domain protein 1 (EPAS1), G protein subunit gamma 2 (GNG2), pantothenate kinase 1 (PANK1), ubiquitin specific peptidase 4 (USP4), G protein subunit alpha q (GNAQ), potassium voltage-gated channel modifier subfamily S member 1 (KCNS1), DNA polymerase gamma 2, accessory subunit (POLG2), NADH:ubiquinone oxidoreductase subunit A10 (NDUFA10), relaxin family peptide receptor 3 (RXFP3), isoprenoid synthase domain containing (ISPD), inositol polyphosphate-5-phosphatase A (INPP5A), sirtuin 7 (SIRT7), guanine monophosphate synthase (GMPS), SIN3-HDAC complex associated factor (SINHCAF), tudor domain containing 1 (TDRD1).
  • Preferably, said gene set is obtained from further filtering the gene set of the invention on genes which encode a protein whereof the level and/or activity can be determined with an available assay. In other words, said gene set is further enriched for candidate drug targets.
  • Generally speaking, the method for determining an age indicator according to the invention and the ensemble of genomic DNA sequences according to the invention are tightly linked and are based on a common inventive concept. Thus, the description and definition of the ensemble of genomic DNA sequences according to the invention herein can be used to further specify the age indicator and/or the reduced training data set of the invention, both of which comprise an ensemble of genomic DNA sequences. Furthermore, said age indicator and/or reduced training data set can be used to further specify the method for determining an age indicator and/or the method for determining the age of an individual. Similarly, the ensemble of genomic DNA sequences according to the invention, which may be comprised in the age indicator of the invention, is preferably obtained by the method for determining an age indicator according to the invention. Moreover, this also applies to the gene set of the invention which preferably is selected from the ensemble of genomic DNA sequences according to the invention.
  • In further preferred aspects, the invention relates to an age indicator obtained by the method for determining an age indicator according to the invention, and/or an ensemble of genomic DNA sequences comprised in said age indicator obtained by said method.
  • In further preferred aspects, the invention relates to an age indicator as described in the Examples herein.
  • As regards the use of the age indicator as described in the examples, the age indicator obtained by the method for determining an age indicator and/or the ensemble of genomic DNA sequences comprised therein, the same applies as is described herein for uses of the ensemble of genomic DNA sequences and/or the gene set according to the invention, in particular in a method for diagnosing the health state and/or the fitness state of an individual and/or in an in silico and/or in vitro screening method for identifying a molecule which affects ageing.
  • In further preferred aspects, the invention relates to a method for diagnosing the health state and/or the fitness state of an individual comprising a step of providing the ensemble of genomic DNA sequences according to the invention, or the gene set according to the invention.
  • Preferably herein, the health state comprises the state of at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer, wherein the state indicates the absence, presence, or stage of the disease or the phenotype associated with a disease. Thus, the health state, as used herein, is preferably related to ageing.
  • Herein, a phenotype associated with an ageing-related disease refers preferably to at least one symptom of an ageing-related disease. Furthermore, an ageing-related diseases or cancer or a phenotype associated therewith, usually progresses is certain stages. Thus, herein, an ageing-related diseases or cancer or a phenotype associated therewith, can be absent or present, or be in a certain stage.
  • In preferred embodiments, the ageing-related disease is Alzheimer's disease, Parkinson's disease, atherosclerosis, cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension, Age-Related Macular Degeneration and/or Benign Prostatic Hyperplasia.
  • Preferably herein, the fitness state comprises the blood pressure, body weight, level of immune cells, level of inflammation and/or the cognitive function of the individual.
  • Preferably herein, the health state and/or fitness state of an individual relates to his biological age. Moreover, the age of the individual which is determined according to the present invention describes said biological age and/or said health state and/or fitness state better than does the chronological age of said individual.
  • In particular, diagnosing the health state and/or fitness state of an individual is complementary to diagnosing one specific disease and/or health/fitness parameter. Primarily, diagnosing the health state and/or fitness state may provide a holistic or integrated perspective on the individual. For example, in case the diagnosis is rather negative, it may be indicated that the individual changes his life style and/or his environment. Moreover, diagnosing the health state and/or fitness state is particularly useful for evaluating if a certain medical treatment or change in the life style or environment of an individual has improved the overall health state and/or fitness state of the individual. It is obvious that the overall health state and/or fitness state of an individual, in particular when related to ageing, is a crucial factor for the wellbeing of said individual. In other words, instead of only assaying the state of individual diseases, the method for diagnosing the health state and/or the fitness state according to the invention may allow diagnosing how young or old the individual biologically is.
  • In certain embodiments, the method for diagnosing the health state and/or the fitness state of an individual further comprises a step of determining the methylation levels of the genomic DNA sequences in a biological sample of said individual comprising said genomic DNA sequences.
  • As regards determining the methylation levels of the genomic DNA sequences and the biological sample, the same applies as has been described above in the context of the methods of the invention for determining an age indicator and/or the age of an individual.
  • The method for diagnosing the health state and/or the fitness state of an individual according to the invention comprises the medical application and/or the non-medical application of said method.
  • In further preferred aspects, the invention relates to an in silico and/or in vitro screening method for identifying a molecule which affects ageing comprising a step of providing the ensemble of genomic DNA sequences according to the invention, or the gene set of the invention. Preferably, the molecule ameliorates, prevents and/or reverses at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer when administered to an individual. Preferably, said screening method is an in vitro method.
  • As regards the ageing-related disease and the phenotype associated therewith, the same applies as has been described above in the context of the method for diagnosing the health state and/or the fitness state of an individual. Furthermore, the prevention of an ageing-related disease and/or the phenotype associated therewith, relates to the maintenance of its absence; the amelioration relates to the slowed down progression through the stages, the maintenance of a stage and/or the regression to an earlier stage; and the reversion relates to the regression to an earlier stage, preferably to the regression to the absence of the disease and/or the phenotype associated therewith.
  • Herein, cancer is a preferred ageing-related disease.
  • In certain embodiments, the screening method of the invention further comprises a step of determining the DNA methylation level of at least one of the genomic DNA sequences comprised in the ensemble of genomic DNA sequences and/or at least one of the genes comprised in the gene set.
  • In preferred embodiments, the identified molecule increases and/or decreases the DNA methylation level of at least one of said genomic DNA sequences or genes in an individual when administered to said individual. Preferably, the DNA methylation levels are altered such that they are associated with a younger chronological age than before alteration.
  • Thus, the ensemble of genomic DNA sequences or the gene set according to the invention can be used for screening molecules, i.e. drug candidates, which alter the methylation state of said sequences or genes in a way which is associated with a younger chronological age than before alteration. For example, when the methylation level of a genomic DNA sequence increases with chronological age, the drug should decrease the methylation level of said genomic DNA sequence. Similarly, when the methylation level of a genomic DNA sequence decreases with chronological age, the drug should increase the methylation level of said genomic DNA sequence.
  • In certain embodiments, the screening method of the invention, wherein the gene set of the invention is provided, further comprises a step of determining the activity of at least one protein encoded by the gene set. Preferably, said gene set only comprises genes which encode a protein.
  • In preferred embodiments, the identified molecules inhibit and/or enhance the activity of at least one protein encoded by the gene set. Preferably, the protein activities are altered such that they are associated with a younger chronological age than before alteration. For example, when the protein activity of a protein encoded by a genomic DNA sequence increases with chronological age, the drug should decrease/inhibit the activity of said protein. Similarly, when the protein activity of a protein encoded by a genomic DNA sequence decreases with chronological age, the drug should increase/enhance the activity of said protein.
  • As used herein, the activity of a protein also encompasses the level of said protein, in particular of its active form.
  • In further preferred aspects, the invention relates to a chip comprising the ensemble of genomic DNA sequences according to the invention, or the gene set of the invention as spots, wherein each sequence is contained in a separate spot. Preferably, the chip is a microarray chip.
  • In further preferred aspects, the invention relates to a kit comprising
    • (a) at least one unique primer pair, wherein of each primer pair one primer is a forward primer binding to the reverse strand and the other primer is a reverse primer binding to the forward strand of one the genomic DNA sequences comprised in the ensemble of genomic DNA sequences according to the invention or one of the genes comprised in the gene set of the invention, and wherein the two nucleotides which are complementary to the 3′ ends of the forward and reverse primers are more than 30 and less than 3000, preferably less than 1000 nucleotides apart;
    • (b) at least one probe which is complementary to one of the genomic DNA sequences comprised in the ensemble of genomic DNA sequences according to the invention or one of the genes comprised in the gene set of the invention; and/or
    • (c) the chip according to the invention.
  • Preferably, said primer pair is used for a polymerase chain reaction (PCR). Said primers may be DNA methylation specific or not. Preferably, said primers are used for a methylation specific PCR method. The DNA methylation levels may be determined by assaying the amplified PCR products, for example by sequencing or by comparing the quantity of the products obtained by different PCRs with primers binding to either methylated or unmethylated sequences. Preferably, said probe is used for a hybridization method, for example an in-situ hybridization method, or a microarray method.
  • In certain embodiments, the primer or probe specifically binds to either methylated or unmethylated DNA, wherein unmethylated cytosines have been converted to uracils.
  • Herein, conversion of unmethylated cytosines to uracils is done preferably by bisulfite treatment.
  • In certain embodiments, the kit further comprises a container for biological material and/or material for a buccal swab.
  • In certain embodiments, the kit further comprises material for extracting, purifying and or amplifying genomic DNA from a biological sample, wherein the material is a spin column and/or an enzyme.
  • In certain embodiments, the kit further comprises hydrogen sulfite.
  • In further preferred aspects, the invention relates to the use of the chip of the invention and/or the kit of the invention for determining the DNA methylation levels of at least one of the genomic DNA sequences comprised in the ensemble of genomic DNA sequences according to the invention and/or one of the genes comprised in the gene set of the invention.
  • In further preferred aspects, the invention relates to the use of the chip of the invention and/or the kit of the invention for diagnosing the health state and/or the fitness state of an individual.
  • In further preferred aspects, the invention relates to the use of the chip of the invention and/or the kit of the invention in an in silico and/or in vitro screening method for identifying a molecule which affects ageing.
  • As regards the diagnosing of the health state and/or the fitness state of an individual and the in silico and/or in vitro screening method for identifying a molecule which affects ageing, the same applies as has been described above in the context of a method for diagnosing the health state and/or the fitness state of an individual and the in silico and/or in vitro screening method for identifying a molecule which affects ageing.
  • In further preferred aspects, the invention relates to a data carrier comprising the age indicator of the invention, the ensemble of genomic DNA sequences according to the invention, and/or the gene set of the invention.
  • In certain embodiments, the kit and/or the data carrier of the invention further comprises a questionnaire for the individual of whom the age is to be determined, wherein the questionnaire can be blank or comprise information about said individual.
  • The invention further relates to the following further aspects and embodiments. In a further aspect, the invention relates to a method of age determination of an individual based on the levels of methylation of genomic DNA sequences found in the individual, comprising the steps of preselecting from genomic DNA sequences having levels of methylation associable with an age of the individual a set of genomic DNA sequences; determining for a plurality of individuals levels of methylation for the preselected genomic DNA sequences; selecting from the preselected set an ensemble of genomic DNA sequences such that the number of genomic DNA sequences in the ensemble is smaller than the number of genomic DNA sequences in the preselected set, wherein the ages of the individuals can be calculated based on the levels of methylation of the sequences of the ensemble, and a statistical evaluation of the ages if calculated indicates an acceptable quality of the calculated ages; determining in a sample of biological material from the individual levels of the methylation of the sequences of the ensemble; calculating an age of the individual based on levels of the methylation of the sequences of the ensemble; determining a measure of the quality of the age calculated; judging whether or not the quality determined is acceptable or not; outputting the age of the individual calculated if the quality is judged to be acceptable; re-selecting genomic DNA sequences for the ensemble in view of the judgment; and, depending on the judgment, amending the group of individuals to include the individual; re-selecting an ensemble of genomic DNA sequences from the preselected subset based on determinations of the levels of the methylation of individuals of the amended group.
  • In some embodiments, an ensemble of genomic DNA sequences is initially used, selected from a number of genomic DNA sequences having levels of methylation associable with an age of the individual; typically, the number of genomic DNA sequences in the ensemble is smaller than the number from which they are selected; then, methylation levels are obtained for the genomic DNA sequences of the ensemble, and from these an age is determined. In the course of a series of age determinations, the composition of the ensemble and/or the way to determine an age based on the methylation levels obtained for the genomic DNA sequences of the ensemble is repeatedly altered based on additional information generated or gained during the series of determinations, in particular based on the methylation levels additionally determined. Note that in some embodiments of the invention, the determination of an age will be based on an evaluation of methylation levels of specific genomic DNA sequences (or CpG loci) from a plurality of individuals, wherein the plurality of individuals comprises the exact individual, for whom the age is to be determined, although that need not be the case.
  • Surprisingly, it has been found that in this manner, significant improvements over the prior art can be achieved.
  • Generally speaking, such an adaption of the ensemble and/or of the (best) way to determine an age based on the respective methylation levels obtained for the genomic DNA sequences of an ensemble currently considered may be altered with every further individual for whom methylation levels and preferably the chronological age are known. Sometimes, this might not be done for every individual, but only for some of these individuals.
  • The adaption could be effected only after the levels of methylation of genomic DNA sequences have been determined for a plurality of more than one additional individual such as 5, 8, 10, 20, 50 or 100 individuals. This would be particularly advantageous where the effort of statistical evaluation to either select certain genomic DNA sequences into an ensemble and/or to determine the best way of age determination based on the methylation levels of certain genomic DNA sequences is substantive.
  • Thus, it is not necessary to only reiterate the composition of the ensemble and/or the best way to determine an age based on the methylation levels in case an outlier is measured.
  • Rather, there is a possibility to judge that the quality according to a (statistical) measure is not acceptable simply because the (statistical) measure indicates that the size of a reference plurality of individuals is smaller than a certain number, for example smaller than the overall number of all individuals for whom methylation levels have been determined and/or for whom methylation levels for the selected genomic DNA sequences have been determined and the chronological age is also known.
  • It is possible to first reiterate the composition of the ensemble and/or the best way to determine an age based on the methylation levels obtained for the genomic DNA sequences prior to the determination of an age of the specific individual and/or to first calculate the age of the additional individuum and to then reiterate the ensemble and/or the best way later on.
  • Herein, the terms “individuum” and “individual” are used interchangeably.
  • If the composition of the ensemble and/or the best way to obtain an age based on the respective methylation levels is to be effected after outputting the age of the individual, the methylation levels can be stored together with additional information about the individuals such as their chronological age (if known), so that the stored information can be used later on in a statistical (re-)evaluation. Accordingly, it is possible to gather such methylation level information for a plurality of additional individuals prior to reiterating the ensemble and/or the best way.
  • As is obvious from the above, basically the invention suggests in one embodiment to improve a determination of an unknown age based on a statistical evaluation of measurements that themselves will yield the unknown result to be determined. Surprisingly, this is not contradictory in itself as by including such information in a reference group, overall improvements of the reliability of the method can be achieved. Accordingly, it has been found that a self-learning approach can be easily implemented.
  • On average, the age determined by the method should, for a large group of individuals, correspond to the average of their chronological ages. Note that the age determined will be a biological age or at least be closer to a biological age, which may be different from the chronological age and will oftentimes only be useful as it varies vis-à-vis the chronological age, because then, it can be determined whether or not a particular individual is aging faster than average.
  • Therefore, any deviation of the age determined according to the best information available vis-à-vis the chronological age is important. The method can be concluded or re-worded to relate to a method of establishing an age difference between a biological and a chronological age known or to assess differences between biological ages obtained by difference measurements and/or methods.
  • It has been found that using the best information available for such a comparison will typically include the largest number available of individuals rather than a pre-defined, fixed number. Overall, the ages determined for one and the same specimen gained from an individual will be altered if the ensemble and/or the best way of determining in age based on the methylation levels obtained for the genomic sequences is changed.
  • Due to such changes, the overall precision and/or variation could be effected, but the invention provides for improvements of overall precision and/or variation due to this.
  • Note that where a specimen is stored in a manner preventing changes to the methylation level, it will be easy to detect changes in an age determined if the measurements are sufficiently free from noise and the changes due to re-iteration are sufficiently large. Accordingly, it has been found that frequently implementation of a self-learning approach of the invention can be easily detected.
  • In a general approach, it is not necessary to actively preselect from all 28 million genomic DNA sequences having levels of methylation known to be associable with an age or adverse health condition of an individual a set of genomic DNA sequences smaller than the known about 28 million sites. Rather, such active preselection should be considered to have been made already if only a limited number of the known sites are evaluated, e.g. due to a method chosen.
  • A preselection can be made by choosing a specific method of determination of methylation levels such as those provided for example by Illumina™ and/or by choosing DNA chips that have a limited collection of spots that each can be used for determination of only one or some but not all genomic DNA sequences found in the individual and having levels of methylation associable with an age. Hence, the decision to use a specific detection method is an implicit preselection.
  • Also, a preselection can be considered to have been made if only data derived in such a manner is evaluated, i.e. if data is evaluated from less than the full app. 28 million sites constitutes the basis of the ensemble and/or set of the preselected set.
  • Typically, the preselected set will be significantly smaller than 28 million different genomic DNA sequences. In particular, while commercially available methods allow determination of levels of methylation of 800,000 (800000) or more different genomic DNA sequences, it will be understood that methods using chips that allow determination of levels of methylation for only a very limited number of different genomic DNA sequences using a collection of specific sites or “spots” are significantly cheaper to use in determination of an age of an individual.
  • For example, in certain methods chips can be used that allow determination of levels of methylation of only one or a few thousand different genomic DNA sequences, preferably even less, in particular not more than 1000 CpG loci, preferably 500 different genomic DNA sequences or CpG loci, preferably less than 200 different genomic DNA sequences or CpG loci, preferably not more than 150 different genomic DNA sequences or CpG loci.
  • It is possible to only determine levels of methylation for those genomic DNA sequences that constitute part of the ensemble. In this case, during reiteration, the composition of the ensemble may either only be altered in that certain genomic DNA sequences that previously had been considered are disconsidered after the reiteration and/or in that the best way to determine an age based on the methylations levels obtained for the genomic sequences of the ensemble itself is altered, for example where regression coefficients obtained from a multivariate (linear) correlation of methylation levels obtained for the genomic DNA sequences of the ensemble with a chronological age of individuals are changed. Also, it would be possible to carry out a determination of levels of methylation of further sequences prior to re-iteration.
  • It is possible to include in each determination of levels of methylation of individuals (some) more genomic DNA sequences (or CpG loci) than those currently constituting part of an ensemble, for example about or at least 10 or about or at least 20 or about or at least 50 more sequences or CpG loci.
  • Still, the number of genomic DNA sequences having levels of methylation associable with an age of the individual and determined for each individual or some individuals without constituting part of a current ensemble will normally be rather small. For example, it is possible to determine the levels of methylation for genomic DNA sequences currently not constituting part of the ensemble for not more than 5 times the number of genomic DNA sequences currently constituting part of the ensemble. Accordingly, where the ensemble for example comprises 100 different genomic DNA sequences, the overall number of different genomic sequences will usually be less than 500. Typically, there are even smaller numbers of additional genomic DNA sequences or CpG loci.
  • In some embodiments, the additional genomic DNA sequences for which levels of methylation associable with an age are determined, although the respective genomic DNA sequences do not constitute part of an ensemble of genomic DNA sequences from which the age is determined is smaller than 400, preferably smaller than 300, in particular smaller than 100 and in particular less than 60, 50 or 40 CpG loci. In addition and/or as an alternative, the ratio of genomic DNA sequences, not constituting part of the ensemble over genomic DNA sequences in the ensemble is preferably smaller than 5, preferably smaller than 4, preferably smaller than 3, preferably smaller than 2. It is noted that the additional sequences that are currently not constituting part of an ensemble but are used to provide additional levels of methylation only in case these might be helpful in a re-iteration will typically be carefully selected as well. This can be done in the preselection.
  • For example, CpG loci might be selected to the set that have methylations levels correlating well with methylation levels of CpG loci that, while also selected into the ensemble, have a very low overall methylation or a high variance. Also, CpG loci could be included known to be indicative for specific adverse lifestyles even though such loci would not be predominant in a statistical multivariate analysis. Furthermore, CpG loci could be selected additionally that are relevant to subsets of an initial reference group.
  • As will be obvious from the above, the exact numbers of the entire set and/or the ensemble will depend on the availability of affordable measurement methods such as sufficiently cheap chips. Also, data processing costs may be prohibitive. It may be preferred to use a chip adapted to determine levels of methylation of genomic DNA sequences having no more than 1000, 500, 200 spots each adapted to be used in determination of methylation levels of a different CpG locus.
  • It is in particular preferred that this chip comprises at least one spot, preferably at least 10, in particular at least 20, 30, 40, 50 60, 70, 80, 90 or 100 and in particular all spots allowing determination of levels of methylation of one or more, in particular at least 20, 30, 40, 50 60, 70, 80, 90 or 100 and in particular all of the following genomic DNA sequences or CpG loci: cg11330075, cg25845463, cg22519947, cg21807065, cg09001642, cg18815943, cg06335143, cg01636910, cg10501210, cg03324695, cg19432688, cg22540792, cg11176990, cg00097800, cg09805798, cg03526652, cg09460489, cg18737844, cg07802350, cg10522765, cg12548216, cg00876345, cg15761531, cg05990274, cg05972734, cg03680898, cg16593468, cg19301963, cg12732998, cg02536625, cg24088134, cg24319133, cg03388189, cg05106770, cg08686931, cg25606723, cg07782620, cg16781885, cg14231565, cg18339380, cg25642673, cg10240079, cg19851481, cg17665505, cg13333913, cg07291317, cg12238343, cg08478427, cg07625177, cg03230469, cg13154327, cg16456442, cg26430984, cg16867657, cg24724428, cg08194377, cg10543136, cg12650870, cg00087368, cg17760405, cg21628619, cg01820962, cg16999154, cg22444338, cg00831672, cg08044253, cg08960065, cg07529089, cg11607603, cg08097417, cg07955995, cg03473532, cg06186727, cg04733826, cg20425444, cg07513002, cg14305139, cg13759931, cg14756158, cg08662753, cg13206721, cg04287203, cg18768299, cg05812299, cg04028695, cg07120630, cg17343879, cg07766948, cg08856941, cg16950671, cg01520297, cg27540719, cg24954665, cg05211227, cg06831571, cg19112204, cg12804730, cg08224787, cg13973351, cg21165089, cg05087008, cg05396610, cg23677767, cg21962791, cg04320377, cg16245716, cg21460868, cg09275691, cg19215678, cg08118942, cg16322747, cg12333719, cg23128025, cg27173374, cg02032962, cg18506897, cg05292016, cg16673857, cg04875128, cg22101188, cg07381960, cg06279276, cg22077936, cg08457029, cg20576243, cg09965557, cg03741619, cg04525002, cg15008041, cg16465695, cg16677512, cg12658720, cg27394136, cg14681176, cg07494888, cg14911690, cg06161948, cg15609017, cg10321869, cg15743533, cg19702785, cg16267121, cg13460409, cg19810954, cg06945504, cg06153788, and cg20088545.
  • In particular, each of said genomic DNA sequences or CpG loci is comprised in a separate spot of said chip. In other words, one spot of said chip is defined by one of said genomic DNA sequences or CpG loci. It will be obvious that it is useful that at least a plurality of those CpG loci are referred to when measuring the methylation level using a chip. In particular, at least 10, preferably at least 20, preferably at least 50, and particularly preferred, all of the above CG loci will constitute part of a set of preselected genomic DNA sequences having levels of methylation associable with an age of the individuum, so that an ensemble of genomic DNA sequences can be easily obtained comprising either all of the above-listed CG loci or, in a preferred embodiment, at least a number or fraction of the above-listed CG loci. In preferred embodiments of the invention, said chip may be used for determining the DNA methylation levels of a set of genomic DNA sequences, in particular the genomic DNA sequences comprised in the reduced training data set according to the invention.
  • In some cases, the CpG Loci will additionally comprise cg27320127, the last CpG loci being known inter alia from WO2012/162139. The CpGs identified above are identified using Illumina™ methylation probe IDs.
  • In certain embodiments, the chip will comprise a low overall number of spots allowing determination of levels of methylation of the following genomic DNA sequences, in particular less than 1600 spots, in particular less than 800 spots, in particular less than 400 spots, preferably less than 200 spots.
  • It should be noted that when defining a set of genomic DNA sequences having levels of methylation associable with an age of the individuum, the set being different from the entirety of genomic DNA sequences of a human being having levels of methylation associable with an age of the individuum, some or all of the CpG loci assumed to be known in the art to have levels of methylation associable with an age of the individuum known in the art, for example those listed in the WO 2012/162139 A1, could be included. However, it is considered that at least 10, preferably 20, particularly preferred 50, 100 and in particular all of the above-listed CpG loci believed to be novel over those known in the art may constitute part of a preselected set of genomic DNA sequences having levels of methylation associable with an age of the individuum and in particular comprising no more than 5000, in particular no more than 2000, in particular no more than 1000, in particular no more than 250 genomic DNA sequences or CpG loci and/or constituting a fraction of at least 10% of the overall number of genomic DNA sequences in a preselected set, preferably at least 10% thereof, and particularly preferred at least 15%, 20%, 25%, 33%, 50%, 66%, 75%, 80%, 100%. So, in preferred cases the CpG loci listed and newly disclosed herein as being relevant will constitute a significant part of the ensemble.
  • It will be noted that the overall number of CG loci considered in a set from which the ensemble is to be selected, will be dependent on the number of different loci measurable easily and, in a cost-effective manner, according to a respective state of the art. For example, prices of DNA chips having oligonucleotides that bind in a measurement process to DNA fragments comprising the respective CpG loci vary strongly with a number of different sites, with the costs dropping significantly from chips having 1000 or more sites to chips having 500, 384, 192 or 96 different sites.
  • It is noted that the numbers of 96 or 384, while in no way restricted, refer to numbers frequently used in current laboratory procedures. It has already been stated that usually the step of preselecting can be considered to have been effected once it has been decided to use not all CpG loci known in the human being but only those easily accessible. Such a step of preselection could thus be made by a referring to the data set comprising only a correspondingly small number of methylation levels.
  • Also it is noted that, determining in a sample of biological material from an individual levels of the methylation of the sequence of the ensemble can be done by referring to measurements that already have been done on the sample. Accordingly, a determination of levels of the methylation of certain sequences could be effected by opening a corresponding data file. The same holds for selecting from the preselected set an ensemble of genomic DNA sequences in a specific manner. This selection should be considered made in case reference is being had to a data base comprising such an ensemble determined by a preceding analysis of reference data from individuals.
  • Regarding the calculation of an age, it is noted that most frequently, the number of genomic DNA sequences in the set and/or in the plurality is rather large, for example because they comprise more than 5, in particular more than 10, in particular at least 50 different genomic DNA sequences. Also, the number of individuals in the group is rather large as well, that is comprising preferably at least 10, preferably at least 50, in particular at least 100, in particular at least 200, and in a preferred embodiment at least 1000 individuals. Thus, usually, mathematical analysis, in particular statistical analysis is needed to determine the best way of calculating an age of an individual based on the levels of the methylation determined. It should be noted that a “best” way of such calculation may not be the absolute best way but can refer to some very good way. In other words, a way of determination may be stated to be a “best” way even though either the calculations are particularly simple and/or because a local extreme of statistical functions has been used instead of an absolute extreme.
  • As is obvious from the above, typically the calculation of an age of an individual based on levels of the methylation of the sequences of the ensemble will be done in a manner where values relating to the level of methylation such as percentages are used to calculate the age based in a manner using also regression coefficients from a multivariate regression, and in particular from a multivariate linear regression. Calculating a measure such as a statistical measure can be effected in different ways. For example, it can be determined whether or not the levels of the methylation of the sequences themselves should be considered reliable. Where levels are exceptionally low, it might not be advisable to use the respective sequences and/or levels of the methylation because, for example, an error in the determination might have occurred (e.g. due to noise in the methylation level measurements), so that the measurements should be disregarded or weighed with a lower weight, compared to other levels. Also, where the levels of methylation are particularly high or low, it might well be that an assumption made during initial calculations such as in a multivariate linear regression assuming a linear correlation between a level of methylation and age will not apply.
  • It should be noted that generally, while the assumption that the levels of methylation correlate linearly with an age of the individual are useful, this need not be the case where very high or very low levels of methylation are observed or where the individual is significantly chronologically younger or older than the average of the individuals in the reference group. It might be useful to determine a more linear correlation by grouping certain individuals before determining how ages of individuals can best be calculated based on the levels of methylation of sequences found in a reference ensemble. For example, it might be advisable to distinguish between male and female individuals, children, teenagers, young adults, middle-aged persons and senior citizens. Also, it might be useful to differentiate e.g. between smokers and nonsmokers, between persons having specific, different nutrition habits such as frequently eating very fat or not, frequently eating fish vs. frequently eating red meat, frequently and/or regularly drinking alcohol or specific alcohols such as alcoholic beverages, such as beer or wine, people exercising regularly or not, people working in adverse environments exposed to pollutants or dangerous materials such as radioactive materials and/or certain chemicals.
  • Thus, calculating a statistical measure of the quality of the age calculated could take into account whether or not a known chronological age deviates from the calculated biological age significantly more than the entirety of deviations obtained for the reference set and/or more than a plurality of other individuals for whom the levels of the methylation of the sequences of the ensemble has been measured. A difference can be considered to be significantly larger, if the significance is at least 2σ, 3σ, 4σ, 5σ or 6σ.
  • Also, the statistical measure of quality could be estimated by determining whether or not the reference set of individuals is sufficiently large. This would not be the case for example where a regression is carried out having a Spearman correlation of less than 0.85, preferably less than 0.90, preferably less than 0.91 and preferably 0.92 with a mean average error (MAE) of more than 6 years, preferably more than 5 years, in particular more than 4 years. It will be understood that it is also possible to estimate a confidence interval for each separate age calculated and that calculating a statistical measure might include the determination of a confidence interval of an age calculated. However, calculating a statistical measure of the quality of the age calculated might also be done easier, for example by determining whether the underlying reference group is large enough. It can be determined that the quality is not high enough if the group is considered to be too small. This can be the case if either the number of individuals in the reference group overall is too low and/or if the number of individuals in the reference group is too low in view of the number of genomic DNA sequences or CpG loci respectively in the preselected set of genomic DNA sequences or in the selected ensemble.
  • It could also be decided that the quality of an age calculated will not be sufficiently high in case not all individuals for whom methylation levels have been determined or not all individuals having certain properties such as being smokers or being female and so forth have been referred to when determining a best way of estimating and calculating an age. In this case, the (statistical) measure would be the number of members in the reference group vis-à-vis the number of individuals for whom levels of methylation and, where applicable, additional information are available.
  • A calculation of such difference could be done by determining that new data has not been entered into the reference group even prior to calculation of an age of the individual. Then, it should be noted that while at least the age of the individual is outputted in case the quality thereof is judged to be acceptable, it is also possible to output the age even where the quality of the calculation is considered dubious or insufficient. For example, it might be useful to output the age of an individual nonetheless because this allows an operator to check whether any specific problem can be detected that easily explains why the quality of the calculated age is to be considered subpar. For example, it might be that the individual has been grouped wrong so that the age has been determined using an ensemble of genomic DNA sequences and regression coefficients obtained for a group of young male strong smokers while the person is an elderly, non-smoking woman. In some embodiments, a plurality of ensembles of CpG loci are defined based on the set and one of these ensembles is selected based on specific information either derived from one or more specific methylation level of CpG loci analyzed and/or an additional information provided independently thereof. Some of the CpG loci in the preselected set can be chosen such that a specific ensemble can be selected. Such provision and/or selection of a specific ensemble from several ensembles should be considered inventive per se. Also, it would be possible to output the age calculated with an explanation to the individual and offer a refund as standard or guaranteed qualities have not been achieved.
  • Also, it would be possible to recalculate the age once a reiteration of the ensemble and/or the best way of obtaining an age based on the levels of methylation of the sequences has been obtained and only then output the age of the individual calculated in an amended manner.
  • Amending the group of individuals usually would be done by including the one or more individuals for whom individual levels of methylation have additionally been determined. However, it would also be possible to exchange individuals or amend the group of individuals by splitting the group and so forth. For example, a case might occur where an initial group of individuals has been rather small so that a differentiation between smokers and non-smokers, males and females, young and old, persons drinking alcohol or not was not advisable, feasible or reasonable. Then, after some time, a large number of measurements will have been carried out and, in some cases, the additional properties such as individuals being smokers or not will have been determined so that then the group can be amended by adding one or some individuals based on their property and by splitting the groups according to such properties.
  • It should be noted that the levels of methylation will change in a large number of living organisms in a manner relating to the age of the organism. However, usually, the method of age determination will be used to determine the age of mammals, in particular primates, in particular human beings. Still, at least a rough estimate of age might be useful, e.g. for other living beings where trading animals that are particularly expensive.
  • In a preferred embodiment, the individual is a human. Of course, this will then also hold for the individuals of the reference group. It has already been indicated above that the numerous steps listed above will require extensive calculations. Therefore, implementing these steps in an automated manner to be executed by a computer is vital. It should be noted that for cases where at least 20 different genomic DNA sequences are considered in the set or the ensemble and where at least 20, preferably 100 individuals form the reference group, calculations without computer implementation are expected to be particularly error-prone so that the results in their entirety must be considered completely useless and unreliable. Also such calculations would neither be affordable in view of costs of computation done by a human being nor acceptable by any individual having to wait for a result. Therefore, executing at least one and preferably all of the calculation and evaluation steps by computers are considered vital.
  • Regarding the way according to which the levels of methylation of genomic DNA sequences found in the individual are determined, reference is made to the following methods known per se in the art methylation sequencing/bisulfate sequencing, PCR-methods, in particular at least one of methylation specific PCR (MSP), real-time methylation specific PCR, quantitative methylation specific PCR (QMSP), COLD-PCR, PCR using a methylated DNA-specific binding protein, targeted multiplex PCR, real-time PCR and microarray-based PCR, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), methylation-sensitive single-strand conformation analysis, methyl-sensitive cut counting (MSCC), base-specific cleavage/MALDI-TOF, e.g. Agena, combined bisulfate restriction analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), micro array-based methods, bead array-based methods, pyrosequencing, direct sequencing without bisulfate treatment (nanopore technology).
  • It is anticipated by the inventors that, using upcoming technologies or technologies that are known but thus far have found little use or market acceptance, further ways of determination of methylation levels may become available. Therefore, the list of methods given is not exclusive. Also, it might be possible to use different methods of determining methylation levels for different CpGs. Also, it might be possible to use different methods of determining methylation levels for a preselection and for a selection.
  • Among those methods of detecting the levels of methylation in a manner usable for the present invention, the following are currently particularly preferred: methylation sequencing/bisulfate sequencing, methylation specific PCR (MSP), real-time methylation specific PCR, quantitative methylation specific PCR (QMSP), COLD-PCR, base-specific cleavage/MALDI-TOF, e.g. Agena, micro array-based methods, bead array-based methods, pyrosequencing.
  • In some embodiments, the group of individuals for whom levels of methylation are initially determined is sufficiently large to obtain calculated ages that remain sufficiently stable even if the self-learning still leads to significant process. In other words, while an initial training of the process by reiterating the ensemble selection and/or the best way of obtaining results should relate on at least 50 individuals, so as to have sufficiently stable values for initial reference, it usually is preferred to have larger numbers such as 100 or 200 individuals in a reference group before starting actual measurements. As has been indicated above, reiterating the composition of the ensemble and all the best way of calculating an age therefrom can be postponed after a sufficiently large number of additional individuals can be additionally considered or added to the reference group.
  • In some embodiments, the number of genomic DNA sequences in the preselected set can be made rather small while still allowing to amend the ensemble in a useful manner.
  • In some embodiments, the preselected set will on the one hand comprise at least 90 CpG loci, preferably at least 100 CpG loci, particularly preferred at least 140 CpG loci, in particular at least 150 CpG loci.
  • It should be noted that where a broad spectrum of individuals is to be examined, a larger number of CpG loci in the preselected set is advisable, whereas measuring methylation levels in clearly specified, well defined groups might rely on a smaller number of see CpG loci in the preselected set, sometimes even requiring 90 CpG loci or less. On the other hand, the preselected set shall not be excessive for a variety of reasons. First of all, determination of methylation levels of CpG loci is more costly and more complex if more CpG loci are to be examined with respect to the methylation level.
  • Accordingly, a method relying on a large number of CpG loci is costly and reducing the number of CpG loci in an ensemble or in a preselected set does reduce the cost significantly. Also, the data processing is significantly simplified if less CpG loci need to be considered. This holds both for a reiteration of the CpG loci in the ensemble and for the best way of processing methylation obtained for such loci. It is noted that generally, the calculation expands a particular of reiterating the ensemble or best way should be considered to grow in a highly nonlinear manner with a number of genomic DNA sequences considered. Therefore, it is preferred from a data analysis perspective as well to reduce the number of CpG loci considered. However, even where only 350, 170, 150 or even 100 CpG loci are considered in a preselected set, the overall computational effort of a multivariate analysis such as a multilinear regression, a principal component analysis, a partial least square analysis and so forth to determine the most important CpG loci methylation levels without over-determining the system will at any rate not be processable without a computer implementation.
  • It is considered necessary to provide the methylation levels determined in an electronic, automated manner, e.g. by establishing an electronic record or file for the methylation levels that can be used when processing the data even where such data processing is not immediately done after determination of methylation levels; not using computer interfaces for data transmission between the final stage used for obtaining the methylation levels from the samples and the stage used for data analysis would introduce a source of errors that must be considered unacceptable.
  • Therefore, it should be noted that the method generally is a computer implemented method having computer implemented steps and that at least some steps must necessarily be executed using a computer.
  • In some embodiments, the selected ensemble will have a number of CpG loci rather small, in particular comprising less than 150 CpG loci, in particular less than 110 CpG loci, in particular less than 100 CpG loci, and in particular less than 90 CpG loci, in particular less than 80 CpG loci, and in particular less than 70 CpG loci. It has been found that such a relatively small number of CpG loci considered still allows to factor in a large number of different influences, for example from lifestyle, for example due to the food, folate and vitamin intake such as vitamin B12 intake, polyphenols, selenium intake, obesity and/or physical activity, tobacco smoke, alcohol consumption, environmental pollutants such as arsenic and air pollution, aromatic hydrocarbons and other organic pollutants, psychological stress, shift work and so forth. In this respect, reference is made to the paper “Alegria-Torres et al., Epigenomics, 2011 June; 3(3): 267-277”. These authors have shown that lifestyle has a significant influence on epigenetics for a large number of factors and that DNA methylation is influenced by lifestyle.
  • On the other hand, while it is sufficient to have a rather small number of CpG loci considered in the ensemble, the ensemble should not be too small. Otherwise, there is a risk that the age or the deviation of the age determined vis-à-vis the chronological age is affected by measurement errors, an insufficient database in the reference group and so forth. Therefore, in some embodiments, it is advisable to include at least 30 CpG loci in the ensemble, preferably at least 50 CpG loci and in particular at least 60 CpG loci.
  • It should be noted that the numbers indicated above to be suitable for the ensemble are valid after one or more reiterations of the best way of data determination from methylation levels of the see CpG loci of the ensemble.
  • In some embodiments, when reiterating the ensemble, the number of members in the ensemble after reiteration may be different from the number of members in the ensemble prior to reiteration.
  • However, in some embodiments, by such re-iteration, the number of CpG loci in the ensemble may vary optionally, i.e. a mere replacement of one or more CpG loci and the ensemble against one or more other CpG loci in the ensemble is not forbidden.
  • As has been indicated above, usually, the best way to determine an age from the methylation levels of the CpG loci of the ensemble may rely on coefficients obtained by a multiple regression (preferable: multiple linear regression) of the methylation levels against known chronological ages of individuals in the group. In some embodiments, methylation levels are used by considering values that vary between 0% for a minimum methylation of a given CpG locus and 100% of a given CpG locus, the later value being used when the methylation level corresponds to the maximum methylation possible for a given CpG locus. In other words, the methylation level of values are centered and normalized. Of course, rather than using a percentage varying between 0% and 100%, a value between 0 and 1 could also be used. While other ranges of values could be used, using values between 0 and 1 or 0% and 100% is particularly intuitive when assessing results and so forth.
  • As has been stated above, in some embodiments the age of the individual calculated is outputted prior to re-selection of the ensemble independent of the judgement of quality of the measurement.
  • Furthermore, an embodiment exists, wherein if the age of the individual calculated is judged to not be acceptable; and an age is outputted only after a re-selection of the ensemble of genomic DNA sequences has been effected and after an age has been recalculated for the reselected ensemble.
  • Regarding the statistical analysis of the methylation levels or the values relating to the methylation levels, in principle different methods could be used. However, it has been found to be suitable to effect the statistical analysis using at least one regression method, for example a principal component analysis searching for the main components responsible for the deviation of the calculated age, a least square regression, a partial least square regression, a LASSO/elastic net regression and/or an XPG Boost method for identification of relevant CpGs. Of note, as explained further above, LASSO and elastic net are different regression methods, at least because LASSO does not comprise a Ridge regression and/or in elastic net, the L1 regularization parameter is not 1.
  • It is noted that protection is not only sought for the method itself but also for a kit that can be used when a method according to the invention is to be executed, that is a kit for use in such a method.
  • In particular, such a kit will comprise at least a container for biological material of an individual obtained and/or prepared in a manner allowing determination of age according to a method as disclosed herein; the kit also comprising an information carrier carrying information relating to the identification of the patient or individual; the kit further comprising either instructions to execute a method of the invention and/or instructions how to have such a method of the invention executed, e.g. by sending in the probe to a specific lab with a voucher, and/or to provide data for the production of a data carrier comprising age related data determined by a method according to the present invention and/or to provide a data carrier comprising age related data determined by a method according to the present invention.
  • As has been indicated above, while frequently the absolute age of an individual needs to be determined, for example because biological material with DNA from a perpetrator has been sampled at a crime scene in order to provide an estimate of the chronological age of the perpetrator, frequently, it will be preferred to compare the age determined to a known chronological age.
  • Also, it might be useful to assess a difference between a chronological age and a biological age in view of the methylation levels of specific CpG loci for which methylation levels have been determined. It should be noted that these specific CpG loci need not constitute part of the ensemble. For example, certain CpG loci might have a methylation level highly dependent on whether or not a person smokes and whether or not the smoker is a particularly strong smoker.
  • It might not be advisable to include such methylation levels in the ensemble when calculating standard biological age for an individual, but it might be useful to indicate to the individual that certain methylation levels are indicative for environmental or other stress of the individual.
  • For example, the biological age of an individual might be determined by using an ensemble of CpG loci that is particularly useful for non-smokers; this might be useful where the individual has indicated to be a non-smoker. However, a case might occur where a non-smoker has been forced to passively smoke over a long period, for example because of growing up with smoking parents. In that case, the methylation levels of specific CpG loci might have been subjected to substantive change vis-à-vis a true non-smoker so even if otherwise, a correct biological age is determined, it might be useful to indicate to the individual that certain CpG methylation levels indicative of smoking behavior indicate that the person has suffered strongly from (passive) smoking.
  • This shows that in certain cases the preselected set may include additional CpG loci that while not representative for a biological age in a large reference group might still be relevant for a specific individual.
  • It should be noted that given the association of aging behavior and methylation levels, it might be helpful to alter the behavior of the methylation levels. This might be done using appropriate means; inter alia, it is reasonable to assume that drugs might constitute part of such means. Accordingly, where the methylation level has changed for a certain CpG locus vis-à-vis a control group, and it has been found that this change relates to adverse influences, a drug might help to prevent the biochemical adverse effects causing the change of methylation level or to undo the changes.
  • Understanding this, a method of drug screening is also suggested wherein a number of molecules are screened with respect to effecting aging comprising the steps of determining for specific CpG loci whether a molecule of the large number of molecules screened has a positive effect on the methylation levels of the CpG loci. This can be done in particular by a determination effected at least in part in-silico.
  • Thus, it is possible in a method of age determination according to the present invention that after a first ensemble of genomic DNA sequences has been selected and ages are determined for a series of individuals, and wherein for at least some individuals of the series methylation levels of genomic DNA sequences additional to those in the ensemble are determined, the group of individuals is amended to include at least some individuals from the series and a determination is made as to whether the ensemble of genomic DNA sequences should be altered in view of methylation levels obtained for additional genomic DNA sequences that were determined for at least some individuals of the series.
  • Accordingly, the determination of a biological age is altered repeatedly during the course of measurements using more and more data obtained during in the series even if each single determination of the series yields an acceptable result that is a result that has a rather small and easily acceptable confidence interval. The reiteration that is repeatedly executed may, as has been indicated before, relate to only the amendment of regression parameters obtained from a statistical analysis and used in the calculation of an age of an individual, using the methylation levels obtained for the individual or may decide that the ensemble overall should be altered, i.e. additional DNA sequences should be added and/or DNA sequences currently considered should be disconsidered.
  • Even where the results per se are acceptable, it will be understood that the overall quality will improve. However, where the ensemble itself is to be changed by adding additional DNA sequences and where the number of the available genomic DNA sequences from which such a selection into the ensemble can be made is small, care should be taken to define the DNA sequences that form of pool or set from which the selection can be made in a manner so that adding additional sequences actually is helpful. Therefore, at least in some cases, it is considered useful to start with a very large number of genomic DNA sequences having methylation levels associable with age and to then reduce this large number of genomic DNA sequences to be considered so that the selection, particularly if done repeatedly and often during standard measurements such as every can 8th, 10th or 100th individual, or after having x % more individuals that could be added to a reference group such as x=10%, 20%, 25%, 33%. 50%, 66%, 75%, 100%. Thus, the set should be carefully selected and a multiselection step for determining a useful preselection oftentimes may be advisable.
  • For example, first, the methylation levels of genomic DNA sequences of a few hundred individuals could be measured for some 800,000 (800000) different genomic DNA sequences. From the data set obtained, a few thousand genomic DNA sequences could be selected, for example in view of a principal component analysis determining the main components of the data set of methylation levels obtained versus the actual ages of the patient. Then, for the selected few thousand genomic DNA sequences, additional measurements could be effected for several hundred or more, e.g. a few thousand individuals and from the data set thus generated, several hundred genomic DNA sequences could be selected, for example of 384 DNA sequences that will have methylation levels detectable by a DNA chip having 384 different or oligonucleotide spots.
  • Again, the reduction of the number of genomic DNA sequences from the few thousand to 384 genomic DNA sequences could be made in view of a further principal component analysis, in view of the values of the respective methylation levels, in view of several methylation levels of different genomic DNA sequences being highly correlated and so forth.
  • After the final selection is made and the set of genomic DNA sequences is sufficiently small to allow a cheap determination of all methylation levels, which could be the case for 384 different genomic DNA sequences or 96 genomic DNA sequences, from those remaining genomic DNA sequences, the ensemble could be determined, but the determination of methylation levels can be determined for all of the remaining methylation DNA sequences without excessive costs.
  • In some embodiments of the invention, when deciding whether or not the ensemble or the best way of determining an age in view of methylation levels obtained should be altered, the decision is made based on a set of individuals as large as possible. Therefore, it is possible to provide additional data other than the methylation levels of the ensemble for at least some individuals in addition to the individuals of a presently used reference group. Then, a decision as to whether or not the ensemble or the best way of determining an age should be altered is made (also) in view of the methylation levels obtained for the additional individuals.
  • It should be noted that usually, the information relating to the additional individuals is used in such a decision as to the best way of calculating the age or as to the selection of genomic DNA sequences into the ensemble or out of the ensemble by simply enlarging a given group of individuals. However, there may be certain cases where it is useful to simultaneously delete individuals from the reference group or to split the reference group into several groups, each group having individuals with specific properties. One reason to exclude individuals from the reference group previously used could be in that a large number of additional individuals is added to the reference group and by doing so, when analyzing the entire group of both previous and added individuals, previously present individuals might be found to have methylation levels that now constitute statistical outliers.
  • Furthermore, a case might occur where a preselection has been made using a first detection method for detecting methylation levels such as a detection method measuring the methylation levels of some 850000 CpG loci while the actual measurement is performed with a method that is capable of determining the methylation levels of only way less CpG loci, and the methylation levels for these CpG loci show a behavior different from the behavior of the methylation levels of the same CpGs in a cross comparison. Here, while it might be useful to initially rely on the initial measurements obtained by a first means, once a sufficiently large database for the exact second method actually used in providing the methylation levels of the ensemble is available, those data obtained with the more complex first method can be deleted. Other reasons why a deletion might be useful is if a sufficiently large number of individuals have finally been sampled that share a common property and the individual to be deleted from the reference group does not share this property. For example, it is possible to delete individuals that are obese from an initial reference group if after some time it is decided that the ensemble and best way of determining an age should be determined such that best results are obtained for perfectly trained athletes that are not obese.
  • While it is possible to amend the ensemble and/or the best way of age determination based on methylation levels only once data from a large number of individuals is available, it can additionally and/or alternatively be decided that a re-evaluation of the ensemble and/or the best way should be carried out in view of methylation levels for a specific individual if at least one of the following conditions have been met: some or all methylation levels detected in the genomic DNA sequences are considered to be too low, the predicted age of a single individual deviates too far from a known chronological age of the individual, the predicted ages of a number of individuals show a systematic deviation from the known chronological ages of a number of individuals, the predicted ages of a number of individuals are scattered around the known chronological ages of the individuals with a variance considered too large, the predicted ages of a number of individuals show a systematic deviation from the known chronological ages of the individuals, the number of individuals for whom an age has been determined based on a given ensemble has reached a predetermined number, a specified time has elapsed since a previous re-selection.
  • It is possible to decide that reiteration or re-evaluation of the ensemble and/or the best way is necessary immediately and/or it can be decided that such reiteration is postponed until data from a sufficiently large number of such individuals is available where the above-mentioned condition is met. Another reason to postpone reiteration would be that such reiteration is only carried out in specific intervals; basically, in all these cases, information relating to the individuals, in particular the methylation levels detected in the genomic DNA sequences and, preferably the chronological ages of the individuals where known are stored prior to reiteration; then, a reiteration using all stored information is effected.
  • In some embodiments, judgment of the quality of a determined age is done in that a comparison is made with a known chronological age. In most cases, a confidence interval is known that can be taken as a measure of quality. A very broad confidence interval might indicate that the determined age is unreliable. Also, once a large group of individuals has been examined, it is likely that the age determined does not deviate too far from ages of other individuals previously determined. In other words, once a large reference group has been examined and a new individual has a determined biological age that shows an aging behavior way faster or way slower than other individuals aging fast or slow, for whom previously data have been analyzed, it is not unlikely that an error has occurred, in particular if no additional factors influencing aging are known. In such a case, it could be decided that while the age might be correct, the quality thereof cannot be assessed in satisfying manner. Nonetheless, in such a case, the age determined would be indicated to the individual because, even though it cannot be assured that the age determined is reliable, it might be advisable for the individual to act as if the age determined would be reliable. For example, where a particularly fast aging behavior previously not observed in a large group of individuals is observed, so that the quality of the high age relative to the actual chronological age cannot be assessed, it might be necessary for the individual to consult a medical doctor.
  • Accordingly, the invention relates to the following items:
    • 1. A method for determining an age indicator comprising the steps of
    • (a) providing a training data set of a plurality of individuals comprising for each individual
      • (i) the DNA methylation levels of a set of genomic DNA sequences and
      • (ii) the chronological age, and
    • (b) applying on the training data set a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), thereby determining the age indicator and a reduced training data set,
      • wherein the independent variables are the methylation levels of the genomic DNA sequences and preferably wherein the dependent variable is the age,
      • wherein the age indicator comprises
      • (i) a subset of the set of genomic DNA sequences as ensemble and
      • (ii) at least one coefficient per genomic DNA sequence contained in the ensemble, and
      • wherein the reduced training data set comprises all data of the training data set except the DNA methylation levels of the genomic DNA sequences which are eliminated by the LASSO.
    • 2. A method for determining the age of an individual comprising the steps of
    • (a) providing a training data set of a plurality of individuals comprising for each individual
      • (i) the DNA methylation levels of a set of genomic DNA sequences and
      • (ii) the chronological age, and
    • (b) applying on the training data set a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), thereby determining the age indicator and a reduced training data set,
      • wherein the independent variables are the methylation levels of the genomic DNA sequences and preferably wherein the dependent variable is the age,
      • wherein the age indicator comprises
      • (i) a subset of the set of genomic DNA sequences as ensemble and
      • (ii) at least one coefficient per genomic DNA sequence contained in the ensemble, and
      • wherein the reduced training data set comprises all data of the training data set except the DNA methylation levels of the genomic DNA sequences which are eliminated by the LASSO, and
    • (c) providing the DNA methylation levels of the individual for whom the age is to be determined of at least 80%, preferably 100% of the genomic DNA sequences comprised in the age indicator, and
    • (d) determining the age of the individual based on its DNA methylation levels and the age indicator,
    • preferably wherein the determined age can be different from the chronological age of the individual.
    • 3. The method of items 1 or 2, wherein the regression method further comprises applying a stepwise regression subsequently to the LASSO.
    • 4. The method of item 3, wherein the stepwise regression is applied on the reduced training data set.
    • 5. The method of any of items 1 to 4, wherein the ensemble comprised in the age indicator is smaller than the set of genomic DNA sequences.
    • 6. The method of any of items 1 to 5, wherein the ensemble comprised in the age indicator is smaller than the set of genomic DNA sequences comprised in the reduced training data set.
    • 7. The method of any of items 3 to 6 wherein the stepwise regression is a bidirectional elimination, wherein statistically insignificant independent variables, are removed, preferably wherein the significance level is 0.05.
    • 8. The method of any of items 1 to 7, wherein the LASSO is performed with the biglasso R package, preferably by applying the command “cv.biglasso”, preferably wherein the “nfold” is 20.
    • 9. The method of any of items 1 to 8, wherein the regression method does not comprise a Ridge regression (L2 regularization) or the L2 regularization parameter/lambda parameter is 0.
    • 10. The method of any of items 1 to 9, wherein the LASSO L1 regularization parameter/alpha parameter is 1.
    • 11. The method of any of items 1 to 10, wherein the age indicator is iteratively updated comprising adding the data of at least one further individual to the training data in each iteration, thereby iteratively expanding the training data set.
    • 12. The method of item 11, wherein in one updating round the added data of each further individual comprise the individual's DNA methylation levels of
    • (i) at least 5%, preferably 50%, more preferably 100% of the set of genomic DNA sequences comprised in the initial or any of the expanded training data sets, and/or
    • (ii) the genomic DNA sequences contained in the reduced training data set.
    • 13. The method of items 11 or 12, wherein all genomic DNA sequences (independent variables) which are not present for all individuals who contribute data to the expanded training data set are removed from the expanded training data set.
    • 14. The method of any of items 11 to 13, wherein in one updating round the set of genomic DNA sequences whereof the methylation levels are added is identical for each of the further individual(s).
    • 15. The method of any of items 11 to 14, wherein one updating round comprises applying the LASSO on the expanded training data set, thereby determining an updated age indicator and/or an updated reduced training data set.
    • 16. The method of any of items 11 to 15, wherein the training data set to which the data of the at least one further individual are added is the reduced training data set, which can be the initial or any of the updated reduced training data sets.
    • 17. The method of item 16, wherein the reduced training data set is the previous reduced training data set in the iteration.
    • 18. The method of any of items 11 to 17, wherein one updating round comprises applying the stepwise regression on the reduced training data set thereby determining an updated age indicator.
    • 19. The method of any of items 1 to 18, wherein in one updating round, the data of at least one individual is removed from the training data set and/or the reduced training data set.
    • 20. The method of any of items 11 to 19, wherein the addition and/or removal of the data of an individual depends on at least one characteristic of the individual, wherein the characteristic is the ethnos, the sex, the chronological age, the domicile, the birth place, at least one disease and/or at least one life style factor, wherein the life style factor is selected from drug consumption, exposure to an environmental pollutant, shift work or stress.
    • 21. The method of any of items 1 to 20, wherein the quality of the age indicator is determined, wherein the determination of said quality comprises the steps of
    • (a) providing a test data set of a plurality of individuals who have not contributed data to the training data set comprising for each said individual
      • (i) the DNA methylation levels of the set of genomic DNA sequences comprised in the age indicator and
      • (ii) the chronological age; and
    • (b) determining the quality of the age indicator by statistical evaluation and/or evaluation of the domain boundaries,
    • wherein the statistical evaluation comprises
      • (i) determining the age of the individuals comprised in the test data set,
      • (ii) correlating the determined age and the chronological age of said individual(s) and determining at least one statistical parameter describing this correlation, and
      • (iii) judging if the statistical parameter(s) indicate(s) an acceptable quality of the age indicator or not, preferably wherein the statistical parameter is selected from a coefficient of determination (R2) and a mean absolute error (MAE), wherein a R2 of greater than 0.50, preferably greater than 0.70, preferably greater than 0.90, preferably greater than 0.98 and/or a MAE of less than 6 years, preferably less than 4 years, preferably at most 1 year, indicates an acceptable quality, and wherein evaluation of the domain boundaries comprises
      • (iv) determining the domain boundaries of the age indicator,
        • wherein the domain boundaries are the minimum and maximum DNA methylation levels of each genomic DNA sequence comprised in the age indicator and wherein said minimum and maximum DNA methylation levels are found in the training data set which has been used for determining the age indicator, and
      • (v) determining if the test data set exceeds the domain boundaries, wherein not exceeding the domain boundaries indicates an acceptable quality.
    • 22. The method of any of items 1 to 21, wherein the training data set and/or the test data set comprises at least 10, preferably at least 30 individuals, preferably at least 200 individuals, preferably wherein the training data set comprises at least 200 individuals and the test data set at least 30 individuals.
    • 23. The method of items 21 or 22, wherein the age indicator is updated when its quality is not acceptable.
    • 24. The method of any of items 11 to 23, wherein the age of the individual is determined based on its DNA methylation levels and the updated age indicator.
    • 25. The method of any of items 2 to 24, wherein the age of the individual is only determined with the age indicator when he/she has not contributed data to the training data set which is used for generating said age indicator.
    • 26. The method of any of items 1 to 25, wherein the age indicator is not further updated when the number of individuals comprised in the data has reached a predetermined value and/or a predetermined time has elapsed since a previous update.
    • 27. The method of any of items 1 to 26, wherein the set of genomic DNA sequences comprised in the training data set is preselected from genomic DNA sequences whereof the methylation level is associable with chronological age.
    • 28. The method of item 27, wherein, the preselected set comprises at least 400000, preferably at least 800000 genomic DNA sequences.
    • 29. The method of any of items 1 to 28, wherein the genomic DNA sequences comprised in the training data set are not overlapping with each other and/or only occur once per allele.
    • 30. The method of any of items 1 to 29, wherein the reduced training data set comprises at least 90, preferably at least 100, preferably at least 140 genomic DNA sequences.
    • 31. The method of any of items 1 to 30, wherein the reduced training data set comprises less than 5000, preferably less than 2000, preferably less than 500, preferably less than 350, preferably less than 300 genomic DNA sequences.
    • 32. The method of any of items 1 to 31, wherein the age indicator comprises at least 30, preferably at least 50, preferably at least 60, preferably at least 80 genomic DNA sequences.
    • 33. The method of any of items 1 to 32, wherein the age indicator comprises less than 300, preferably less than 150, preferably less than 110, preferably less than 100, preferably less than 90 genomic DNA sequences.
    • 34. The method of any of items 1 to 33, wherein the DNA methylation levels of the genomic DNA sequences of an individual are measured in a sample of biological material of said individual comprising said genomic DNA sequences.
    • 35. The method of item 34, wherein the sample comprises buccal cells.
    • 36. The method of any of items 34 or 35, further comprising a step of obtaining the sample, wherein the sample is obtained non-invasively.
    • 37. The method of any of items 34 to 36, wherein the DNA methylation levels are measured by methylation sequencing, bisulfate sequencing, a PCR method, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), methylation-sensitive single-strand conformation analysis, methyl-sensitive cut counting (MSCC), base-specific cleavage/MALDI-TOF, combined bisulfate restriction analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), micro array-based methods, bead array-based methods, pyrosequencing and/or direct sequencing without bisulfate treatment (nanopore technology).
    • 38. The method of any of items 34 to 37, wherein the DNA methylation levels of genomic DNA sequences of an individual are measured by base-specific cleavage/MALDI-TOF and/or a PCR method, preferably wherein base-specific cleavage/MALDI-TOF is the Agena technology and the PCR method is methylation specific PCR.
    • 39. The method of any of items 34 to 38, wherein the DNA methylation levels of the genomic DNA sequences comprised in the age indicator are determined in a sample of biological material comprising said genomic DNA sequences of the individual for whom the age is to be determined.
    • 40. An ensemble of genomic DNA sequences comprising at least 10, preferably at least 50, preferably at least 70, preferably all of cg11330075, cg25845463, cg22519947, cg21807065, cg09001642, cg18815943, cg06335143, cg01636910, cg10501210, cg03324695, cg19432688, cg22540792, cg11176990, cg00097800, cg27320127, cg09805798, cg03526652, cg09460489, cg18737844, cg07802350, cg10522765, cg12548216, cg00876345, cg15761531, cg05990274, cg05972734, cg03680898, cg16593468, cg19301963, cg12732998, cg02536625, cg24088134, cg24319133, cg03388189, cg05106770, cg08686931, cg25606723, cg07782620, cg16781885, cg14231565, cg18339380, cg25642673, cg10240079, cg19851481, cg17665505, cg13333913, cg07291317, cg12238343, cg08478427, cg07625177, cg03230469, cg13154327, cg16456442, cg26430984, cg16867657, cg24724428, cg08194377, cg10543136, cg12650870, cg00087368, cg17760405, cg21628619, cg01820962, cg16999154, cg22444338, cg00831672, cg08044253, cg08960065, cg07529089, cg11607603, cg08097417, cg07955995, cg03473532, cg06186727, cg04733826, cg20425444, cg07513002, cg14305139, cg13759931, cg14756158, cg08662753, cg13206721, cg04287203, cg18768299, cg05812299, cg04028695, cg07120630, cg17343879, cg07766948, cg08856941, cg16950671, cg01520297, cg27540719, cg24954665, cg05211227, cg06831571, cg19112204, cg12804730, cg08224787, cg13973351, cg21165089, cg05087008, cg05396610, cg23677767, cg21962791, cg04320377, cg16245716, cg21460868, cg09275691, cg19215678, cg08118942, cg16322747, cg12333719, cg23128025, cg27173374, cg02032962, cg18506897, cg05292016, cg16673857, cg04875128, cg22101188, cg07381960, cg06279276, cg22077936, cg08457029, cg20576243, cg09965557, cg03741619, cg04525002, cg15008041, cg16465695, cg16677512, cg12658720, cg27394136, cg14681176, cg07494888, cg14911690, cg06161948, cg15609017, cg10321869, cg15743533, cg19702785, cg16267121, cg13460409, cg19810954, cg06945504, cg06153788, and cg20088545, or a fragment thereof which comprises at least 70%, preferably at least 90% of the continuous nucleotide sequence.
    • 41. The ensemble of genomic DNA sequences of item 39 comprising at least 4, preferably at least 10, preferably at least 30, preferably at least 70, preferably all of cg11330075, cg00831672, cg27320127, cg27173374, cg14681176, cg06161948, cg08224787, cg05396610, cg15609017, cg09805798, cg19215678, cg12333719, cg03741619, cg16677512, cg03230469, cg19851481, cg10543136, cg07291317, cg26430984, cg16950671, cg16867657, cg22077936, cg08044253, cg12548216, cg05211227, cg13759931, cg08686931, cg07955995, cg07529089, cg01520297, cg00087368, cg05087008, cg24724428, cg19112204, cg04525002, cg08856941, cg16465695, cg08097417, cg21628619, cg09460489, cg13460409, cg25642673, cg19702785, cg18506897, cg21165089, cg27540719, cg21807065, cg18815943, cg23677767, cg07802350, cg11176990, cg10321869, cg17343879, cg08662753, cg14911690, cg12804730, cg16322747, cg14231565, cg10501210, cg09275691, cg15008041, cg05812299, cg24319133, cg12658720, cg20576243, cg03473532, cg07381960, cg05106770, cg04320377, cg19432688, cg22519947, cg06831571, cg08194377, cg01636910, cg14305139, cg04028695, cg15743533, cg03680898, cg20088545, cg13333913, cg19301963, cg13973351, cg16781885, cg04287203, cg27394136, cg10240079, cg02536625, and cg23128025, or a fragment thereof which comprises at least 70%, preferably at least 90% of the continuous nucleotide sequence.
    • 42. The ensemble of genomic DNA sequences of item 41 comprising at least 4, preferably at least 10, preferably all of cg11330075, cg00831672, cg27320127, cg27173374, cg14681176, cg06161948, cg08224787, cg05396610, cg15609017, cg09805798, cg19215678, cg12333719, cg03741619, cg03230469, cg19851481, cg10543136, cg07291317, cg26430984, cg16950671, cg16867657, cg13973351, cg16781885, cg04287203, cg27394136, cg10240079, cg02536625, and cg23128025.
    • 43. The ensemble of genomic DNA sequences of items 41 or 42 comprising at least 4, preferably all of cg11330075, cg00831672, cg27320127, cg10240079, cg02536625, and cg23128025.
    • 44. The ensemble of genomic DNA sequences of any of items 40 to 43 comprising the complementary sequences thereof in addition and/or in place of said ensemble of genomic DNA sequences.
    • 45. A gene set comprising at least 10, preferably at least 30, preferably at least 50, preferably at least 70, preferably all of SIM bHLH transcription factor 1 (SIM1), microtubule associated protein 4 (MAP4), protein kinase C zeta (PRKCZ), glutamate ionotropic receptor AMPA type subunit 4 (GRIA4), BCL10, immune signaling adaptor (BCL10), 5′-nucleotidase domain containing 1 (NT5DC1), suppression of tumorigenicity 7 (ST7), protein kinase C eta (PRKCH), glial cell derived neurotrophic factor (GDNF), muskelin 1 (MKLN1), exocyst complex component 6B (EXOC6B), protein S (PROS1), calcium voltage-gated channel subunit alpha1 D (CACNA1D), kelch like family member 42 (KLHL42), OTU deubiquitinase 7A (OTUD7A), death associated protein (DAP), coiled-coil domain containing 179 (CCDC179), iodothyronine deiodinase 2 (DIO2), transient receptor potential cation channel subfamily V member 3 (TRPV3), MT-RNR2 like 5 (MTRNR2L5), filamin B (FLNB), furin, paired basic amino acid cleaving enzyme (FURIN), solute carrier family 25 member 17 (SLC25A17), Gpatch domain containing 1 (GPATCH1), UDP-GlcNAc:betaGal beta-1,3-Nacetylglucosaminyltransferase 9 (B3GNT9), zyg-11 family member A, cell cycle regulator (ZYG11A), seizure related 6 homolog like (SEZ6L), myosin X (MYO10), acetyl-CoA carboxylase alpha (ACACA), G protein subunit alpha i1 (GNAI1), CUE domain containing 2 (CUEDC2), homeobox D13 (HOXD13), Kruppel like factor 14 (KLF14), solute carrier family 1 member 2 (SLC1A2), acetoacetyl-CoA synthetase (AACS), ankyrin repeat and sterile alpha motif domain containing 1A (ANKS1A), microRNA 7641-2 (MIR7641-2), collagen type V alpha 1 chain (COL5A1), arsenite methyltransferase (AS3MT), solute carrier family 26 member 5 (SLC26A5), nucleoporin 107 (NUP107), long intergenic non-protein coding RNA 1797 (LINC01797), myosin IC (MYO1C), ankyrin repeat domain 37 (ANKRD37), phosphodiesterase 4C (PDE4C), EF-hand domain containing 1 (EFHC1), uncharacterized LOC375196 (LOC375196), ELOVL fatty acid elongase 2 (ELOVL2), WAS protein family member 3 (WASF3), chromosome 17 open reading frame 82 (C17orf82), G protein-coupled receptor 158 (GPR158), F-box and leucine rich repeat protein 7 (FBXL7), ripply transcriptional repressor 3 (RIPPLY3), VPS37C subunit of ESCRT-I (VPS37C), polypeptide Nacetylgalactosaminyltransferase like 6 (GALNTL6), DENN domain containing 3 (DENND3), nuclear receptor corepressor 2 (NCOR2), endothelial PAS domain protein 1 (EPAS1), PBX homeobox 4 (PBX4), long intergenic non-protein coding RNA 1531 (LINC01531), family with sequence similarity 110 member A (FAM110A), glycosyltransferase 8 domain containing 1 (GLT8D1), G protein subunit gamma 2 (GNG2), MT-RNR2 like 3 (MTRNR2L3), zinc finger protein 140 (ZNF140), kinase suppressor of ras 1 (KSR1), protein disulfide isomerase family A member 5 (PDIA5), spermatogenesis associated 7 (SPATA7), pantothenate kinase 1 (PANK1), ubiquitin specific peptidase 4 (USP4), G protein subunit alpha q (GNAQ), potassium voltage-gated channel modifier subfamily S member 1 (KCNS1), DNA polymerase gamma 2, accessory subunit (POLG2), storkhead box 2 (STOX2), neurexin 3 (NRXN3), BMS1, ribosome biogenesis factor (BMS1), forkhead box E3 (FOXE3), NADH:ubiquinone oxidoreductase subunit A10 (NDUFA10), relaxin family peptide receptor 3 (RXFP3), GATA binding protein 2 (GATA2), isoprenoid synthase domain containing (ISPD), adenosine deaminase, RNA specific B1 (ADARB1), Wnt family member 7B (WNT7B), pleckstrin and Sec7 domain containing 3 (PSD3), membrane anchored junction protein (MAJIN), pyridine nucleotide-disulphide oxidoreductase domain 1 (PYROXD1), cingulin like 1 (CGNL1), chromosome 7 open reading frame 50 (C7orf50), MORN repeat containing 1 (MORN1), atlastin GTPase 2 (ATL2), WD repeat and FYVE domain containing 2 (WDFY2), transmembrane protein 136 (TMEM136), inositol polyphosphate-5-phosphatase A (INPP5A), TBC1 domain family member 9 (TBC1D9), interferon regulatory factor 2 (IRF2), sirtuin 7 (SIRT7), collagen type XXIII alpha 1 chain (COL23A1), guanine monophosphate synthase (GMPS), potassium two pore domain channel subfamily K member 12 (KCNK12), SIN3-HDAC complex associated factor (SINHCAF), hemoglobin subunit epsilon 1 (HBE1), and tudor domain containing 1 (TDRD1).
    • 46. The gene set of item 45, comprising at least 5, preferably at least 10, preferably at least 30, preferably all of ISPD, KCNK12, GNG2, SIRT7, GPATCH1, GRIA4, LINC01531, LOC101927577, NCOR2, WASF3, TRPV3, ACACA, GDNF, EFHC1, MYO10, COL23A1, TDRD1, ELOVL2, GNAI1, MAP4, CCDC179, KLF14, ST7, INPP5A, SIM1, SLC1A2, AS3MT, KSR1, DSCR6, IRF2, KCNS1, NRXN3, C11orf85, HBE1, FOXES, TMEM136, HOXD13, LOC375196, PANK1, MIR107, COL5A1, PBX4, ZNF140, GALNTL6, NUP107, LOC100507250, MTRNR2L5, C17orf82, MKLN1, FURIN, KLHL42, MORN1, ANKS1A, BCL10, DENND3, FAM110A, PROS1, WNT7B, FBXL7, GATA2, VPS37C, NRP1, POLG2, ANKRD37, GMPS, and WDFY2.
    • 47. The gene set of item 45 comprising at least 5, preferably at least 10, preferably at least 20, preferably all of microtubule associated protein 4 (MAP4), protein kinase C zeta (PRKCZ), glutamate ionotropic receptor AMPA type subunit 4 (GRIA4), suppression of tumorigenicity 7 (ST7), protein kinase C eta (PRKCH), calcium voltage-gated channel subunit alpha1 D (CACNA1D), death associated protein (DAP), transient receptor potential cation channel subfamily V member 3 (TRPV3), furin, paired basic amino acid cleaving enzyme (FURIN), acetyl-CoA carboxylase alpha (ACACA), G protein subunit alpha i1 (GNAI1), solute carrier family 1 member 2 (SLC1A2), phosphodiesterase 4C (PDE4C), ELOVL fatty acid elongase 2 (ELOVL2), nuclear receptor corepressor 2 (NCOR2), endothelial PAS domain protein 1 (EPAS1), G protein subunit gamma 2 (GNG2), pantothenate kinase 1 (PANK1), ubiquitin specific peptidase 4 (USP4), G protein subunit alpha q (GNAQ), potassium voltage-gated channel modifier subfamily S member 1 (KCNS1), DNA polymerase gamma 2, accessory subunit (POLG2), NADH:ubiquinone oxidoreductase subunit A10 (NDUFA10), relaxin family peptide receptor 3 (RXFP3), isoprenoid synthase domain containing (ISPD), inositol polyphosphate-5-phosphatase A (INPP5A), sirtuin 7 (SIRT7), guanine monophosphate synthase (GMPS), SIN3-HDAC complex associated factor (SINHCAF), tudor domain containing 1 (TDRD1).
    • 48. The ensemble of genomic DNA sequences of any of items 40 to 44 or the gene set of any of items 45 to 47 which is obtained by the method of items 2 to 39,
    • wherein the ensemble of genomic DNA sequences is comprised in the reduced training data set and/or the age indicator according to the method, and
    • wherein said gene set is obtained by selecting from said ensemble of genomic DNA sequences those which encode a protein, or a microRNA or long non-coding RNA.
    • 49. The ensemble of genomic DNA sequences of any of items 40 to 44 or 48, or the gene set of any of items 45 to 48 for use in diagnosing the health state of an individual.
    • 50. The ensemble of genomic DNA sequences or the gene set for use according to item 49,
    • wherein the health state comprises the state of at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer,
    • wherein the state indicates the absence, presence, or stage of the disease or the phenotype associated with a disease.
    • 51. The ensemble of genomic DNA sequences or the gene set for use according to item 50,
    • wherein the ageing-related disease is Alzheimer's disease, Parkinson's disease, atherosclerosis, cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension, Age-Related Macular Degeneration and/or Benign Prostatic Hyperplasia.
    • 52. Use of the ensemble of genomic DNA sequences of any of items 40 to 44 or 48, or the gene set of any of items 45 to 48 for determining the fitness state of an individual.
    • 53. The use of item 52, wherein the fitness state comprises the blood pressure, body weight, level of immune cells, level of inflammation and/or the cognitive function of the individual.
    • 54. A method for diagnosing the health state and/or the fitness state of an individual comprising a step of providing the ensemble of genomic DNA sequences of any of items 40 to 44 or 48, or the gene set of any of items 45 to 48.
    • 55. The method of item 54, further comprising a step of determining the methylation levels of the genomic DNA sequences in a biological sample of the individual comprising said genomic DNA sequences.
    • 56. The method of any of items 54 or 55, wherein the health state comprises the state of at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer,
    • preferably wherein the ageing-related disease is Alzheimer's disease, Parkinson's disease, atherosclerosis, cardiovascular disease, cancer, arthritis, cataracts, osteoporosis, type 2 diabetes, hypertension, Age-Related Macular Degeneration and/or Benign Prostatic Hyperplasia, and/or
    • the fitness state comprises the blood pressure, body weight, level of immune cells, level of inflammation and/or the cognitive function of the individual.
    • 57. The method of any of items 55 or 56, wherein the biological sample is obtained noninvasively, preferably by a buccal swab.
    • 58. An in silico and/or in vitro screening method for identifying a molecule which affects ageing comprising a step of providing the ensemble of genomic DNA sequences of any of items 40 to 44 or 48, or the gene set of any of items 45 to 48,
    • wherein the molecule ameliorates, prevents and/or reverses at least one ageing-related disease, at least one phenotype associated with at least one ageing-related disease, and/or cancer when administered to an individual.
    • 59. The method of item 58, further comprising a step of determining the DNA methylation level of at least one of the genomic DNA sequences.
    • 60. The method of items 58 or 59, wherein the identified molecule increases and/or decreases the DNA methylation level of at least one of the genomic DNA sequences in an individual when administered to said individual.
    • 61. The method of item 60, wherein the DNA methylation levels are altered such that they are associated with a younger chronological age than before alteration.
    • 62. The method of any of items 58 to 61, wherein the gene set of items 45 to 48 is provided, and wherein said method further comprises a step of determining the activity of at least one protein encoded by the gene set.
    • 63. The method of item 62, wherein the identified molecules inhibit and/or enhance the activity of at least one protein encoded by the gene set.
    • 64. The method of item 63, wherein the protein activities are altered such that they are associated with a younger chronological age than before alteration.
    • 65. A chip comprising the ensemble of genomic DNA sequences of any of items 40 to 44 or 48, or the gene set of any of items 45 to 48 as spots, wherein each sequence is contained in a separate spot.
    • 66. A kit comprising at least one unique primer pair,
    • wherein of each primer pair one primer is a forward primer binding to the reverse strand and the other primer is a reverse primer binding to the forward strand of one the genomic DNA sequences comprised in the ensemble of genomic DNA sequences of any of items 40 to 44 or 48 or one of the genes comprised in the gene set of items any of 45 to 48,
    • and wherein the two nucleotides which are complementary to the 3′ ends of the forward and reverse primers are more than 30 and less than 3000, preferably less than 1000 nucleotides apart.
    • 67. A kit comprising at least one probe which is complementary to one of the genomic DNA sequences comprised in the ensemble of genomic DNA sequences of any of items 40 to 44 or 48 or one of the genes comprised in the gene set of any of items 45 to 48.
    • 68. The kit of items 65 or 66, wherein the primer or probe specifically binds to either methylated or unmethylated DNA, wherein unmethylated cytosines have been converted to uracils.
    • 69. A kit comprising the chip of item 65.
    • 70. The kit of any of items 51 to 57, further comprising a container for biological material and/or material for a buccal swab.
    • 71. The kit of any of items 66 to 70, further comprising material for extracting, purifying and or amplifying genomic DNA from a biological sample, wherein the material is a spin column and/or an enzyme.
    • 72. The kit of any of items 66 to 71, further comprising hydrogen sulfite.
    • 73. A data carrier comprising the age indicator obtained by the method of any of items 2 to 39, the ensemble of genomic DNA sequences of any of items 40 to 44 or 48, and/or the gene set of any of items 45 to 48.
    • 74. The kit of any of items 66 to 72 or the data carrier of item 73, further comprising a questionnaire for the individual of whom the age is to be determined, wherein the questionnaire can be blank or comprise information about said individual.
    • 75. The method of any of items 1 to 39, wherein the training data set, reduced training data set and/or added data further comprise at least one factor relating to a life-style or risk pattern associable with the individual(s).
    • 76. The method of item 75, wherein the factor is selected from drug consumption, environmental pollutants, shift work and stress.
    • 77. The method of any of items 75 or 76, wherein the training data set and/or the reduced training data set is restricted to sequences whereof the DNA methylation level and/or the activity/level of an encoded proteins is associated with at least one of the life-style factors.
    • 78. The method of any of items 75 to 77, further comprising a step of determining at least one life-style factor which is associated with the difference between the determined and the chronological age of said individual.
  • In further aspects, the invention relates to the following items:
  • Item No. 79 relates to a method of age determination of an individual based on the levels of methylation of genomic DNA sequences found in the individual, comprising the steps of
      • preselecting
        • from genomic DNA sequences having levels of methylation associable with an age of the individual a set of genomic DNA sequences;
      • determining for a plurality of individuals levels of methylation for the preselected genomic DNA sequences;
      • selecting from the preselected set an ensemble of genomic DNA sequences such that
        • the number of genomic DNA sequences in the ensemble is smaller than the number of genomic DNA sequences in the preselected set,
        • ages of the individuals can be calculated based on the levels of methylation of the sequences of the ensemble, and
        • a statistical evaluation of the ages calculated indicates an acceptable quality of the calculated ages;
      • determining in a sample of biological material from the individual levels of the methylation of the sequences of the ensemble;
      • calculating an age of the individual based on levels of the methylation of the sequences of the ensemble;
      • calculating a statistical measure of the quality of the age calculated;
      • judging whether or not the quality according to the statistical measure is acceptable or not;
      • outputting the age of the individual calculated if the quality is judged to be acceptable;
      • determining that a re-selection of genomic DNA sequences is necessary if the quality is judged to be not acceptable,
      • amending the group of individuals to include the individual;
      • re-selecting an ensemble of genomic DNA sequences from the preselected subset based on determinations of the levels of the methylation of individuals of the amended group.
  • Furthermore, the invention has been disclosing an item 80 relating to a method of age determination according to above listed, numbered item 79 wherein the individual is a human.
  • Furthermore, the invention has been disclosing an item No. 81 relating to a method of age determination according to one of the preceding above listed, numbered items, wherein at least one step is a computer implemented step,
      • in particular at least one of the steps of
      • and preferably all of the steps of
      • selecting from the preselected set an ensemble of genomic DNA sequences
        • such that
          • the number of genomic DNA sequences in the ensemble is smaller than the number of genomic DNA sequences in the preselected set,
          • ages of the individuals can be calculated based on the levels of methylation of the sequences of the ensemble,
          • and
          • a statistical evaluation of the ages calculated indicates an acceptable quality of the calculated ages;
      • determining in a sample of biological material from the individual levels of the methylation of the sequences of the ensemble;
      • calculating an age of the individual based on levels of the methylation of the sequences of the ensemble;
      • calculating a statistical measure of the quality of the age calculated;
      • judging whether or not the quality according to the statistical measure is acceptable or not;
      • outputting the age of the individual calculated if the quality is judged to be acceptable;
      • determining that a re-selection of genomic DNA sequences is necessary if the quality is judged to be not acceptable,
      • amending the group of individuals to include the individual;
      • re-selecting an ensemble of genomic DNA sequences from the preselected subset based on determinations of the levels of the methylation of individuals of the amended group.
  • Furthermore, the invention has been disclosing an item No. 82 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the levels of methylation of genomic DNA sequences found in the individual are measured by at least one of methylation sequencing/bisulfate sequencing, a PCR—method, in particular at least one of methylation specific PCR (MSP), real-time methylation specific PCR, quantitative methylation specific PCR (QMSP), COLD-PCR, PCR using a methylated DNA-specific binding protein, targeted multiplex PCR, real-time PCR and microarray-based PCR, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), methylation-sensitive single-strand conformation analysis, methyl-sensitive cut counting (MSCC), base-specific cleavage/MALDI-TOF, e.g. Agena, combined bisulfate restriction analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), micro array-based methods, bead array-based methods, pyrosequencing, direct sequencing without bisulfate treatment (nanopore technology).
  • Furthermore, the invention has been disclosing an item No. 83 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the levels of methylation of genomic DNA sequences are measured by at least one of
      • methylation sequencing/bisulfate sequencing, methylation specific PCR (MSP), real-time methylation specific PCR, quantitative methylation specific PCR (QMSP), COLD-PCR, base-specific cleavage/MALDI-TOF, e.g. Agena, micro array-based methods, bead array-based methods, pyrosequencing.
  • Furthermore, the invention has been disclosing an item No. 84 suggesting a method of age determination according to one of the previous above listed, numbered items, wherein
      • the plurality of individuals for whom levels of methylation for the preselected genomic DNA sequences are determined comprises at least 50, preferably at least 100, in particular at least 200 individuals.
  • Furthermore, the invention has been disclosing an item No. 85 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the group of individuals is amended by adding the individual to the group.
  • Furthermore, the invention has been disclosing an item No. 86 relating to a method of age determination according to one of the previous above listed, numbered items, wherein amending the group of individuals to include the individual comprises eliminating at least one other individual from the group, in particular in view of factors unrelated to their age and/or methylation levels of some or all of their genomic DNA sequences.
  • Furthermore, the invention has been disclosing an item No. 87 relating to a method of age determination according to one of the previous above listed, numbered items,
      • wherein after a first ensemble of genomic DNA sequences has been selected, ages are determined for a series of individuals,
      • and wherein for at least some individuals of the series methylation levels of genomic DNA sequences additional to those in the ensemble are determined,
      • the group of individuals is amended to include at least some individuals from the series and a determination is made as to whether the ensemble of genomic DNA sequences should be altered in view of methylation levels obtained for additional genomic DNA sequences that were determined for at least some individuals of the series.
  • Furthermore, the invention has been disclosing an item No. 88 relating to a method of age determination according to the previous above listed, numbered item, wherein
      • for at least some individuals the methylation levels of all genomic DNA sequences in the preselected set are determined,
      • and wherein the determination as to whether the ensemble of genomic DNA sequences should be altered is made in view of the methylation levels of all of these methylation levels obtained for the at least some individuals.
  • Furthermore, the invention has been disclosing an item No. 89 relating to a method of age determination according to the previous above listed, numbered item, wherein a determination is made to alter the ensemble based on methylation levels obtained for additional individuals if at least one or preferably several of the following conditions have been met:
      • some or all methylation levels detected in the genomic DNA sequences are considered to be too low,
      • the predicted age of a single individual deviates too far from a known chronological age of the individual,
      • the predicted ages of a number of individuals show a systematic deviation from the known chronological ages of a number of individuals,
      • the predicted ages of a number of individuals are scattered around the known chronological ages of the individuals with a variance considered too large,
      • the predicted ages of a number of individuals show a systematic deviation from the known chronological ages of the individuals,
      • the number of individuals for whom an age has been determined based on a given ensemble has reached a predetermined number,
      • a specified time has elapsed since a previous re-selection.
  • Furthermore, the invention has been disclosing an item No. 90 relating to a method of age determination according to one of the previous above listed, numbered items, wherein judging whether or not the quality according to the statistical measure is acceptable or not comprises a statistical evaluation of the ages taking into account the known chronological ages of at least part of the individuals, in particular a statistical evaluation taking into account if a predicted age of a single individual deviates too far from a known chronological age of the individual, in particular vis-à-vis a known outlier behavior.
  • Furthermore, the invention has been disclosing an item No. 91 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the preselected set comprises at least 90 genomic DNA sequences, preferably at least 100 genomic DNA sequences, particularly preferred at least 140 genomic DNA sequences and/or the preselected set comprises less than 2000 genomic DNA sequences, in particular less than 500 genomic DNA sequences, in particular less than 350 genomic DNA sequences, in particular less than 170 genomic DNA sequences, in particular less than 150 genomic DNA sequences.
  • Furthermore, the invention has been disclosing an item No. 92 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the selected ensemble comprises at least 30 genomic DNA sequences, preferably at least 50 genomic DNA sequences, particularly preferred at least 60 genomic DNA sequences and/or the selected ensemble comprises less than 150 genomic DNA sequences, in particular less than 110 genomic DNA sequences, in particular less than 100 genomic DNA sequences, in particular less than 90 genomic DNA sequences, in particular less than 80 genomic DNA sequences, in particular less than 70 genomic DNA sequences.
  • Furthermore, the invention has been disclosing an item No. 93 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the reselected ensemble comprises at least 30 genomic DNA sequences, preferably at least 50 genomic DNA sequences, particularly preferred at least 60 genomic DNA sequences and/or the selected ensemble comprises less than 150 genomic DNA sequences, in particular less than 110 genomic DNA sequences, in particular less than 100 genomic DNA sequences, in particular less than 90 genomic DNA sequences, in particular less than 80 genomic DNA sequences, in particular less than 70 genomic DNA sequences.
  • Furthermore, the invention has been disclosing an item No. 94 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the number of genomic DNA sequences in the re-selected ensemble is different from the number of genomic DNA sequences in the initially selected ensemble.
  • Furthermore, the invention has been disclosing an item No. 95 relating to a method of age determination according to one of the previous above listed, numbered items, wherein at least one genomic DNA sequence included in the selected ensemble is not included in the genomic DNA sequences of the re-selected ensemble.
  • Furthermore, the invention has been disclosing an item No. 96 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the age is determined from a statistical analysis of the methylation levels of the genomic DNA sequences of the ensemble in view of known ages of individuals in the group, in particular by using coefficients obtained for respective genomic DNA sequences of the ensemble in a multiple linear regression of methylation level values against known ages of individuals in the group.
  • Furthermore, the invention has been disclosing an item No. 97 relating to a method of age determination according to one of the previous above listed, numbered items, wherein methylation level values are determined from methylation levels by centering and/or normalizing obtained levels and wherein the methylation level values are subjected to the statistical analysis.
  • Furthermore, the invention has been disclosing an item No. 98 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the age of the individual calculated is outputted prior to re-selection of the ensemble independent of the judgement of quality of the measurement.
  • Furthermore, the invention has been disclosing an item No. 99 relating to a method of age determination according to one of the previous above listed, numbered items, wherein the age of the individual calculated is judged to not be acceptable and an age is outputted only after a reselection of the ensemble of genomic DNA sequences has been effected and after an age has been recalculated for the re-selected ensemble.
  • Furthermore, the invention has been disclosing an item No. 100 suggesting a method of age determination according to one of the previous above listed, numbered items, wherein the selection of genomic DNA sequences is based on a statistical analysis of values relating to methylation levels of genomic DNA sequences of the individuals, in particular a statistical analysis using at least one regression method for identification of relevant CpG loci, in particular at least one of a principal component analysis, a LASSO/elastic net regression and/or an XPG Boost method for identification of relevant CpGs.
  • Furthermore, the invention has been disclosing an item No. 101 relating to a kit comprising at least a container for biological material of an individual obtained and/or prepared in a manner allowing determination of age according to one of the preceding method above listed, numbered items; the kit also comprising an information carrier carrying information relating to the identification of the patient; the kit further comprising instructions to execute or how to have executed a method according to one of the preceding method above listed, numbered items and/or to provide data for the production of a data carrier comprising age related data determined by a method according to a previous method above listed, numbered item and/or to provide a data carrier comprising age related data determined by a method according to a previous method above listed, numbered item.
  • Furthermore, the invention has been disclosing an item No. 102 relating to a method of assessing a difference between a chronological age and a biological age, the method comprising determining an age based on methylation levels according to a method according to one of the preceding method above listed, numbered items and comparing the determined biological age to a known chronological age.
  • Furthermore, the invention has been disclosing an item No. 103 relating to a method of assessing a difference between a chronological age and a biological age according to the previous above listed, numbered items, wherein for a plurality of individuals a difference is determined, values of factors that may or may not affect the differences are determined for the plurality of individuals and factors having a large influence on the difference between a chronological age and the biological age in a large number of individuals are determined.
  • Furthermore, the invention has been disclosing an item No. 104 relating to a method of screening a number of molecules with respect to effecting aging comprising the steps of determining a number of genomic DNA sequences that correlate well to a biological age, in particular by referring to genomic DNA sequences selected for an ensemble in the method of above listed, numbered item 79, and determining whether a molecule of the number of molecules has a positive effect on the methylation levels of the genomic DNA sequences, in particular by an in-silico determination.
  • Furthermore, the invention has been disclosing an item No. 105 relating to a method of determination of an age of an individual based on an evaluation of methylation levels of selected genomic DNA sequences from a plurality of individuals, wherein the plurality of individuals comprises the individual.
  • Furthermore, the invention has been disclosing an item No. 106 relating to a chip comprising a number of spots, in particular less than 500, preferably less than 385, in particular less than 193, in particular less than 160 spots, adapted for use in determining methylation levels, the spots comprising at least one spot and preferably several spots specifically adapted to be used in the determination of methylation levels of at least one of cg11330075, cg25845463, cg22519947, cg21807065, cg09001642, cg18815943, cg06335143, cg01636910, cg10501210, cg03324695, cg19432688, cg22540792, cg11176990, cg00097800, cg09805798, cg03526652, cg09460489, cg18737844, cg07802350, cg10522765, cg12548216, cg00876345, cg15761531, cg05990274, cg05972734, cg03680898, cg16593468, cg19301963, cg12732998, cg02536625, cg24088134, cg24319133, cg03388189, cg05106770, cg08686931, cg25606723, cg07782620, cg16781885, cg14231565, cg18339380, cg25642673, cg10240079, cg19851481, cg17665505, cg13333913, cg07291317, cg12238343, cg08478427, cg07625177, cg03230469, cg13154327, cg16456442, cg26430984, cg16867657, cg24724428, cg08194377, cg10543136, cg12650870, cg00087368, cg17760405, cg21628619, cg01820962, cg16999154, cg22444338, cg00831672, cg08044253, cg08960065, cg07529089, cg11607603, cg08097417, cg07955995, cg03473532, cg06186727, cg04733826, cg20425444, cg07513002, cg14305139, cg13759931, cg14756158, cg08662753, cg13206721, cg04287203, cg18768299, cg05812299, cg04028695, cg07120630, cg17343879, cg07766948, cg08856941, cg16950671, cg01520297, cg27540719, cg24954665, cg05211227, cg06831571, cg19112204, cg12804730, cg08224787, cg13973351, cg21165089, cg05087008, cg05396610, cg23677767, cg21962791, cg04320377, cg16245716, cg21460868, cg09275691, cg19215678, cg08118942, cg16322747, cg12333719, cg23128025, cg27173374, cg02032962, cg18506897, cg05292016, cg16673857, cg04875128, cg22101188, cg07381960, cg06279276, cg22077936, cg08457029, cg20576243, cg09965557, cg03741619, cg04525002, cg15008041, cg16465695, cg16677512, cg12658720, cg27394136, cg14681176, cg07494888, cg14911690, cg06161948, cg15609017, cg10321869, cg15743533, cg19702785, cg16267121, cg13460409, cg19810954, cg06945504, cg06153788, and cg20088545.
  • Furthermore, the invention has been disclosing an item No. 107 relating to a method of determination of an age indicator for an individual in a series of individuals, the determination being based on levels of methylation of genomic DNA sequences found in the individual, wherein based on methylation levels of an ensemble of genomic DNA sequences selected from a set of genomic DNA sequences having levels of methylation associable with an age of the individuals an age indicator for the individual is provided in a manner relying on a statistical evaluation of levels of methylation for genomic DNA sequences of the plurality of individuals, characterized in that the age indicator for the individual is provided in a manner relying on a statistical evaluation of levels of methylation for genomic DNA sequences of a plurality of individuals which is different from the plurality of individuals that was referred to for a preceding statistical evaluation used for the determination of the same age indicator of an individual preceding in the series, the difference of plurality of individuals being caused in that a plurality of individuals used for the first statistical evaluations is amended at least by inclusion of at least one additional preceding individual from the series, and wherein preferably the age indicator for the individual is provided in a manner where the at least two different statistical evaluations of the two different plurality of individuals result in a change of at least one coefficient used when calculating the age indicator from the methylation levels of an ensemble and/or result in levels of methylation of different genomic DNA sequences or CgP loci found being considered.
  • In some aspects, a method of determination of an age indicator for an individual in a series of individuals based on levels of methylation of genomic DNA sequences is disclosed, wherein an ensemble of genomic DNA sequences is selected and an age indicator for the individual is provided in a manner continuously improving a statistical evaluation of previous measurements to obtain a better model.
    • BRIEF DESCRIPTION OF THE FIGURES
  • FIG. 1. Performance of LASSO. A set of 148 cg sites was determined as optimal. Shown are four plots referring to Lasso regression and its performances. In all four plots a vertical dotted line represents the automatic threshold chosen for the number of variables selected. All plots report mean values plus range intervals produced by 20 cross validation runs. The different axes show different model metrics according to the biglasso package. The two upper plots report sums of cross-validated errors and coefficient of determination (R2), while the bottom two plots report two particular parameter from R implementation of LASSO regression: signal-to-noise ratio and <bs>. Details are in https://cran.rstudio.com/web/packages/biglasso/biglasso.pdf
  • FIG. 2. Performance of the age indicator obtained by LASSO and subsequent stepwise regression. Shown are the chronological age (actual age) and the determined age (predicted age) of 259 individuals of the training data set and 30 individuals of the test data set. No relevant or significant differences between training and test data set were observed. The shown coefficient of variation R2 is based on the training and test data merged.
  • FIG. 3. Correlations of representative CpG sites with the chronological age. Individuals of training and test data merged were grouped based on their chronological age (>48 years, 25-48 years, and <25 years; “old”, “mid” and “young”, respectively). The distributions of DNA methylation levels (“value”) are shown for 8 representative CpG sites per age group. The genes comprised in the CpG sites are annotated.
  • FIG. 4. Overlap of CG sites with the set of CG sites as described by Horvath in Genome Biology 2013, 14:R115. The Venn diagram reports the amount of overlap between the set of 148 genomic DNA sequences (CpGs) determined herein by applying LASSO (IME-Cerascreen) and the 353 CpG List reported by Horvath in Genome Biology 2013, 14:R115. See also FIG. 5.
  • FIG. 5. Overlap of CG sites determined herein by applying LASSO (IME-Cerascreen) and subsequent stepwise regression (IME_Cerascreen_8). Also shown is the overlap with the set of CG sites as described by Horvath in Genome Biology 2013, 14:R115. See also FIG. 4.
    •  EXAMPLES Example 1: Measuring CpG Methylation Levels of DNA from Biological Samples
  • For a very large number of app. 850.000 (850000) CpGs, the respective methylation levels have been measured in the following way:
  • Buccal cells were collected from a number of test persons with buccal swabs and genomic DNA was purified from the buccal cells using a QIAamp 96 DNA Swab BioRobot Kit (Qiagen, Hilden, Germany). The purified genomic DNA was treated with sodium bisulfite using the Zymo EZ DNA Methylation Kit (Zymo, Irvine, Calif., USA). This treatment converts unmethylated cytosines to uracil, while methylated cytosines remain unchanged.
  • All further steps were performed with components from the Infinium MethylationEPIC Kit (Illumina™, San Diego, Calif., USA) according to the manufacturer's instructions. In short, bisulfite-treated samples were denatured and neutralized to prepare them for amplification. The amplified DNA was then isothermally amplified in an overnight step and enzymatically fragmented. Fragmented DNA was precipitated with isopropanol, collected by centrifugation at 4° C. and resuspended in hybridization buffer. The fragmented, resuspended DNA samples were then dispensed onto an Infinium MethylationEPIC BeadChip (Illumina™) and the BeadChip was incubated overnight in the Illumina™ Hybridization Oven to hybridize the samples onto the BeadChip by annealing the fragments to locus-specific 50mers that are covalently linked to the beads.
  • Unhybridized and nonspecifically hybridized DNA was washed away and the BeadChip was prepared for staining and extension in a capillary flow-through chamber. Single-base extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates fluorescent labels on the BeadChip and thereby determines the methylation level of the query CpG sites. The BeadChip was scanned with the iScan System, using a laser to excite the fluorophore of the single-base extension product on the beads and recording high resolution images of the light emitted from the fluorophores. The data was analyzed using the GenomeStudio Methylation Module (Illumina™), which allows the calculation of beta-values for each analyzed CpG.
  • With this procedure, the methylation levels of more than 850′000 (850000) different Illumina™ defined CpGs were measured per sample and person and a numerical value for each methylation level of the more than 850′000 (850000) different CpGs was provided. This was done for a large number of samples, each sample from a different individual. The numerical values have been normalized such that 0 corresponds to minimum methylation possible for a CpG and 1 corresponds to the maximum methylation for the CpG. Of note, 1 also corresponds to 100% or full methylation.
    • Example 2: Measuring CpG Methylation Levels by Base-Specific Cleavage/MALDI-TOF (Agena)
  • To determine methylation levels of a pre-selected set of several hundred different CpGs, the EpiTYPER DNA Methylation Analysis Kit from Agena Bioscience (San Diego, Calif., USA) was used. In the example, 384 methylation levels of 384 different CpGs have been determined.
  • Again, Buccal cells were collected from a number of persons with buccal swabs and genomic DNA was purified from the buccal cells using a QIAamp 96 DNA Swab BioRobot Kit (Qiagen, Hilden, Germany). The purified genomic DNA was treated with sodium bisulfite using the Zymo EZ DNA Methylation Kit (Zymo, Irvine, Calif., USA). This treatment converts unmethylated cytosines to uracil, while methylated cytosines remain unchanged.
  • Subsequently, the target regions containing the CpGs of interest were amplified by PCR using a specific primer pair per target region, each containing a T7-promoter-tagged reverse primer, respectively.
  • The PCR products were then treated with shrimp alkaline phosphatase to remove the unreacted nucleotides from the sample and in vitro transcribed using T7 RNA polymerase. The resulting RNA transcripts were specifically cleaved at uracil residues and dispensed onto a SpectroCHIP Array. This chip was placed into a MALDI-TOF mass spectrometer for data acquisition and the resulting data was analyzed with EpiTYPER software.
  • From the results, a numerical value for each methylation levels of the 384 different CpGs was provided. The numerical value was again normalized such that 0 corresponds to minimum methylation possible for a CpG and 1 (100%) corresponds to the maximum methylation for the CpG.
  • While methylation levels of 384 different genomic DNA sequences were determined by the method of Example 2, compared to the app. 850.000 (850000) different genomic DNA sequences, it is noted that the cost of an analysis according to Example 2 is significantly lower, amounting to less than 1/5 of the costs at the time of application.
    • Example 3: Measuring CpG Methylation Levels by Methylation Specific PCR (msPCR)
  • To determine methylation levels of a pre-selected set of 192 different CpGs, real-time quantitative methylation specific PCR (msPCR) was performed in the following manner:
  • For each of the 192 CpG-containing target regions to be analyzed, a specific set of three oligonucleotides was designed, containing one forward primer and two reverse primers. The two reverse primers were designed such that one is having a G at the 3′ end that is complementary to the methylated, unchanged C while the second forward primer is having an A at the 3′ end that is complementary to the converted uracil.
  • Then, buccal cells were collected from a number of persons with buccal swabs and genomic DNA was purified from the buccal cells using a QIAamp 96 DNA Swab BioRobot Kit (Qiagen, Hilden, Germany). The purified genomic DNA was treated with sodium bisulfite using the Zymo EZ DNA Methylation Kit (Zymo, Irvine, Calif., USA). This treatment converts unmethylated cytosines to uracil, while methylated cytosines remain unchanged.
  • To determine methylation levels of CpGs contained in the sample, for each set of three oligonucleotides two PCR reactions were initiated, the first PCR reaction using the forward and the first of the two reverse primers, the second PCR reaction using the forward and the second of the two reverse primers. The methylation level of each CpG was determined, using real-time quantitative msPCR with TaqMan probes specific for each amplified target region.
  • From the results, a numerical value for each methylation levels of the 192 different CpGs was provided. The numerical value was again normalized such that 0 corresponds to minimum methylation possible for a CpG and 1 (100%) corresponds to the maximum methylation for the CpG.
  • While the number of different genomic DNA sequences is lower than in the method of Example 2, the method is extremely competitive with respect to costs.
    • Example 4: Generation of an Age Predictor Using LASSO
  • DNA methylation levels of 289 individuals (259 for the training data set and 30 for the test data set) have been determined as described in Example 1 unless noted differently. In brief, the DNA methylation levels of 850000 different genomic DNA sequences have been determined from buccal swab samples using the Infinium MethylationEPIC BeadChip (Illumina™). The methylation levels were normalized as beta values using program R v3.4.2, and thus could have a value between 0 and 1. The data set, i.e. the training data set, was a data matrix with a structure as in Table 1.
  • TABLE 1
    Chronological
    ID age CG1 CG2 . . . CG850000
    Individual
    1 28 0.2 1.0 . . . 0.1
    Individual 2  8 . . . . . . . . . . . .
    . . . . . . . . . . . . . . . . . .
    Individual 65 . . . . . . . . . . . .
    259
  • Using the statistical software R v3.4.1 and the biglasso package, a LASSO regression was performed using the command
      • cvfit<-cv.biglasso(Vars800bm, Age, seed=2401, nfolds=20),
        wherein Vars800bm is the training data set which relates to an exemplarily matrix as shown in Table 1, wherein the cg sites are the independent variables and the age is the dependent variable to be modeled; seed is a number used by random generator; and nfolds is the number of cross-validation repetition which the model has to be build with. The value 20 was used for cross-validation. The biglasso package was: “The biglasso Package: A Memory- and Computation-Effic Solver for LASSO Model Fitting with Big Data in R” by Yaohui Zeng and Patrick Breheny in arXiv:1701.05936v2 [statCO] 11 Mar. 2018.
  • The formula of the obtained model (age indicator) upon LASSO regression was:

  • Age=+53.9126*cg27320127+43.1588*cg16267121+31.5464*cg00831672+30.4384*cg27173374+26.5197*cg16867657+20.9302*cg14681176+19.0975*cg25606723+16.8674*cg11607603+16.6092*cg08097417+15.0595*cg11330075+14.5786*cg12333719+14.1955*cg10543136+13.6743*cg21807065+12.4988*cg19851481+12.1954*cg08224787+11.7822*cg19702785+11.7706*cg13759931+11.6845*cg19112204+11.4521*cg07955995+10.869*cg18815943+10.829*cg24724428+10.7537*cg22101188+10.4571*cg19215678+9.551*cg22519947+9.5225*cg06161948+9.3932*cg16677512+9.2647*cg05396610+8.9059*cg21628619+8.7864*cg15609017+8.6846*cg24954665+8.5015*cg25642673+8.284*cg07802350+7.9408*cg05087008+7.8335*cg12548216+7.7144*cg09965557+7.6203*cg16999154+7.6057*cg12238343+7.5126*cg08044253+7.0673*cg16465695+6.939*cg13206721+6.6733*cg09001642+6.1215*cg11176990+6.0675*cg07625177+6.0657*cg05292016+5.9961*cg16593468+5.9511*cg07291317+5.5409*cg18506897+5.4739*cg07120630+5.2279*cg08662753+5.1938*cg24088134+5.1655*cg00097800+4.8623*cg16950671+4.6431*cg16245716+4.6364*cg06279276+4.6224*cg08686931+4.1089*cg27540719+4.0082*cg07529089+3.9294*cg06945504+3.8147*cg23677767+3.7304*cg07766948+3.7296*cg00876345+3.541*cg05972734+3.5305*cg22540792+3.4169*cg08118942+3.1845*cg02032962+3.1329*cg09460489+3.0723*cg22444338+3.0498*cg08856941+2.8317*cg03741619+2.7707*cg03230469+2.6979*cg06153788+2.6678*cg10522765+2.6533*cg14911690+2.5934*cg06186727+2.5488*cg03526652+2.5152*cg01520297+2.4409*cg09805798+2.3836*cg07513002+2.3539*cg08960065+2.3285*cg06335143+2.3044*cg16673857+2.2379*cg05990274+2.0254*cg04525002+1.9303*cg13154327+1.8016*cg07494888+1.7889*cg03388189+1.7543*cg08478427+1.7476*cg18768299+1.6312*cg21165089+1.6196*cg17665505+1.613*cg13460409+1.5347*cg14305139+1.4346*cg12804730+1.2032*cg04875128+1.2025*cg05211227+1.1767*cg18737844+1.1712*cg21460868+1.15*cg26430984+1.135*cg10321869+1.0067*cg14756158+1.0021*cg16322747+0.9948*cg17343879+0.9605*cg22077936+0.7994*cg18339380+0.5436*cg00087368+0.3003*cg05812299+0.281*cg12732998+0.0507*cg16456442+0.0277*cg17760405+0.0165*cg12658720−0.2038*cg08457029−0.4098*cg21962791−0.4232*cg15761531−0.4506*cg19810954−0.4626*cg20425444−0.5866*cg23128025−0.6731*cg25845463−0.6945*cg03324695−1.0445*cg01636910−1.4555*cg12650870−1.8012*cg01820962−2.2813*cg07782620−2.4468*cg04320377−2.6024*cg09275691−2.6286*cg15008041−2.7124*cg20576243−3.4046*cg13973351−3.5199*cg08194377−3.5713*cg07381960−4.0608*cg10240079−4.2758*cg14231565−4.8117*cg24319133−4.8449*cg03680898−5.694*cg19301963−6.83*cg03473532−7.515*cg13333913−8.0702*cg05106770−8.3397*cg04287203−9.4713*cg27394136−9.4931*cg10501210−10.8424*cg19432688−12.9786*cg02536625−13.2229*cg04028695−14.2271*cg16781885−14.728*cg15743533−14.9252*cg04733826−15.7917*cg20088545−16.5954*cg06831571−367.4866.
  • This age indicator comprised 148 terms such as +16.6092*cg08097417, wherein a positive sign indicated that the methylation level positively correlated with age, and a negative sign indicated that the methylation level negatively correlated with age. A numbered cg refers to a genomic DNA sequence according to the Infinium MethylationEPIC BeadChip; and the absolute value of the coefficient with which the cg is multiplied indicates the importance of this cg.
  • Various model performance checks confirmed that the selection of 148 cg sites was optimal (FIG. 1).
  • This age indicator had the following performances: R2=0.72, variable selected=148 (nonzero coefficients), wherein R2 is the coefficient of determination. The statistics have been determined with an independent test data set consisting of data of 30 individuals (about 10%) which were different from the 259 (289-30) individuals used for the training data set but which were drawn from the same population as said 289 individuals.
  • Furthermore, LASSO has been applied on the data of 64 or 150 individuals from the 289 individuals (Table 2).
  • TABLE 2
    Number of selected
    Size of training variables in Performance of age indicator
    data set age indicator with test data set (R2)
    64 30 0.39
    150 105 0.6
    259 148 0.72
  • This suggested that the performance of the LASSO increased when data of further individuals were iteratively added to the data set and the age indicator was iteratively updated.
    • Example 5: Generation of an Age Predictor Using LASSO and Subsequent Stepwise Regression
  • Stepwise regression was applied on a reduced training data set obtained after performing LASSO (Example 4) to distill the best significant set of cg sites/CpGs and thereby optimize the model. The reduced training data set (IME_blasso[,−1]) was the same as the training data set used in Example 4 except that it retained only the 148 columns relating to the 148 cg sites selected by LASSO.
  • Stepwise regression was performed using the statistical software R v3.4.1 and the following command:
  • model_blasso<-step(lm(Age˜., data=IME_blasso[,−1]), direction=“both”), wherein the direction for removing not significant variables was “both”, meaning that both adding and removing variables was allowed.
  • The formula of the obtained model (age indicator) upon LASSO regression and subsequent stepwise regression was:

  • Age=+66.2822*cg11330075+65.203*cg00831672+55.7265*cg27320127+44.4116*cg27173374+38.3902*cg14681176+37.8069*cg06161948+36.6564*cg08224787+31.9397*cg05396610+30.1919*cg15609017+28.089*cg09805798+27.9392*cg19215678+27.8502*cg12333719+27.226*cg03741619+27.0323*cg16677512+25.9599*cg03230469+25.3932*cg19851481+24.5374*cg10543136+22.5525*cg07291317+21.8666*cg26430984+20.3621*cg16950671+20.3269*cg16867657+19.7973*cg22077936+18.7137*cg08044253+18.2047*cg12548216+18.1936*cg05211227+18.0812*cg13759931+17.6857*cg08686931+17.5303*cg07955995+16.1143*cg07529089+14.8703*cg01520297+14.6684*cg00087368+14.4397*cg05087008+14.4361*cg24724428+14.3055*cg19112204+14.2968*cg04525002+14.2302*cg08856941+13.3831*cg16465695+11.8127*cg08097417+11.7798*cg21628619+11.3523*cg09460489+11.2461*cg13460409+10.6268*cg25642673+10.4347*cg19702785+9.7844*cg18506897+9.5931*cg21165089+9.093*cg27540719+8.9361*cg21807065+8.8577*cg18815943+8.6138*cg23677767+7.1699*cg07802350+7.0528*cg11176990+6.5416*cg10321869+6.5049*cg17343879+5.8296*cg08662753+5.696*cg14911690+3.2983*cg12804730+3.1388*cg16322747−4.8653*cg14231565−5.5608*cg10501210−6.047*cg09275691−6.35*cg15008041−9.1942*cg05812299−9.3144*cg24319133−9.4566*cg12658720−9.8704*cg20576243−10.4082*cg03473532−10.6429*cg07381960−11.1592*cg05106770−12.0021*cg04320377−12.3296*cg19432688−12.9858*cg22519947−13.7116*cg06831571−13.8029*cg08194377−13.8668*cg01636910−14.6975*cg14305139−15.0408*cg04028695−16.3295*cg15743533−16.3314*cg03680898−18.6196*cg20088545−19.0952*cg13333913−19.3068*cg19301963−21.5752*cg13973351−23.0892*cg16781885−26.0415*cg04287203−32.3606*cg27394136 48.0918*cg10240079−50.0227*cg02536625−63.4434*cg23128025−519.3495.
  • The meaning of the terms and statistics is as explained in Example 4. Further details on the cg sequences and the coefficients can be found in Table 6.
  • Thus, the number of variables selected was further reduced upon applying the stepwise regression. In fact, the age indicator contained only 88 genomic DNA sequences (cg sites/CpGs).
  • Moreover, the performance of the age indicator obtained by LASSO and subsequent stepwise regression was:
    • R2=0.9884 with the training data; and R2=0.9929 (with the test data set containing the data of 30 test individuals as explained in Example 4). Thus, the performance was enhanced over the age indicator obtained by LASSO without stepwise regression.
  • The performance on the test data was as good as on the training data set which suggests that the age indicator has an outstanding performance (FIG. 2). Moreover, such a high coefficient of determination value indicates a significant improvement over prior art age indicators.
  • By grouping individuals (training and test data sets merged) based on their chronological age, it could be confirmed that the methylation level of representative cg sites selected by the regression analysis correlated well with the age groups (FIG. 3).
  • The age indicator and its determination was then compared to the age indicator of Horvath, Genome Biology 2013, 14:R115 in Table 3:
  • TABLE 3
    Horvath, Genome Biology
    Characteristics
    2013, 14: R115 Present invention
    Sample Various cell types Buccal swabs
    Starting number of cg sites/ 450000 850000
    Illumina ™ chip
    Algorithm Elastic net LASSO + stepwise
    regression
    No. of cg sites used in model   353 88
    No. of cross-validation runs Unknown 20
    Coefficient of determination 0.83 (buccal epithelium) 0.996
    (R2) 0.83 (saliva)
    Median absolute deviation 0.8 (buccal epithelium) 1.0
    (years) 2.7 (saliva)
    p-value of coefficients Unknown p < 0.05
  • This confirmed that the age indicator obtained by LASSO+stepwise regression performed as least as good as a relevant prior art age indicator, or even better, despite having only about 25% of the number of genomic DNA sequences (independent variables).
  • The small set of genomic DNA sequences comprised in the age indicator allows to use alternative, i.e. simpler, methods (see Examples 2 and 3) to determine the DNA methylation levels of individuals for whom the age is to be determined.
  • Moreover the set of cg sites determined by LASSO alone or with LASSO+subsequent stepwise regression had very little overlap with the cg sites determined in Horvath, Genome Biology 2013, 14:R115 (FIGS. 4 and 5).
    • Example 6: Determination of Gene Sets from the Sets of Cg Sites/CpGs
  • The list of cg sites determined by applying LASSO (Example 4) or LASSO+stepwise regression (Example 5) was filtered for those cg sites which were fully contained within a gene. In a first list (Table 4), 106 (partially redundant) coding sequences and non-coding sequences such as miRNAs or long non-coding RNAs were selected based on the 148 CpGs determined by LASSO:
  • TABLE 4
    Illumina ID UCSC_RefGene_Accession Name of first accession No.
    cg00087368 NM_005068 SIM bHLH transcription factor 1 (SIM1)
    cg12548216 NM_030885; microtubule associated protein 4 (MAP4)
    NM_001134364;
    NM_002375
    cg25845463 NM_001033582; protein kinase C zeta (PRKCZ)
    NM_002744;
    NM_001033581
    cg05087008 NM_001077243; glutamate ionotropic receptor AMPA type subunit 4
    NM_001112812; (GRIA4)
    NM_001077244;
    NM_000829
    cg05396610 NR_046356; glutamate ionotropic receptor AMPA type subunit 4
    NM_001077243; (GRIA4)
    NM_000829
    cg01636910 NM_003921 BCL10, immune signaling adaptor (BCL10)
    cg01820962 NM_152729 5′-nucleotidase domain containing 1 (NT5DC1)
    cg07529089 NM_018412; suppression of tumorigenicity 7 (ST7)
    NM_021908
    cg02032962 NM_006255 protein kinase C eta (PRKCH)
    cg03230469 NM_000514 glial cell derived neurotrophic factor (GDNF)
    cg03473532 NM_001145354 muskelin 1 (MKLN1)
    cg03526652 NM_015189 exocyst complex component 6B (EXOC6B)
    cg03680898 NM_000313 protein S (PROS1)
    cg05990274 NM_000720; calcium voltage-gated channel subunit alpha1 D
    NM_001128840; (CACNA1D)
    NM_001128839
    cg04320377 NM_020782 kelch like family member 42 (KLHL42)
    cg04875128 NM_130901 OTU deubiquitinase 7A (OTUD7A)
    cg17665505 NM_004394 death associated protein (DAP)
    cg05211227 NM_001195637 coiled-coil domain containing 179 (CCDC179)
    cg05292016 NM_000793; iodothyronine deiodinase 2 (DIO2)
    NR_038355
    cg03741619 NM_145068 transient receptor potential cation channel subfamily
    V member 3 (TRPV3)
    cg05812299 NM_001190478 MT-RNR2 like 5 (MTRNR2L5)
    cg05972734 NM_001164319; filamin B (FLNB)
    NM_001164318;
    NM_001457;
    NM_001164317
    cg07381960 NM_002569; furin, paired basic amino acid cleaving enzyme
    NM_001289823 (FURIN)
    cg06153788 NR_104238; solute carrier family 25 member 17 (SLC25A17)
    NR_104235;
    NR_104237;
    NR_104236;
    NM_006358;
    NM_001282727;
    NM_001282726
    cg06161948 NM_018025 G-patch domain containing 1 (GPATCH1)
    cg06279276 NM_033309 UDP-GlcNAc: betaGal beta-1,3-N-
    acetylglucosaminyltransferase 9 (B3GNT9)
    cg06335143 NM_001004339 zyg-11 family member A, cell cycle regulator
    (ZYG11A)
    cg06945504 NM_001184776; seizure related 6 homolog like (SEZ6L)
    NM_001184775;
    NM_001184774;
    NM_001184777;
    NM_001184773;
    NM_021115
    cg07291317 NM_012334 myosin X (MYO10)
    cg16677512 NM_198838; acetyl-CoA carboxylase alpha (ACACA)
    NM_198837;
    NM_198839;
    NM_198836;
    NM_198834
    cg08044253 NM_002069; G protein subunit alpha i1 (GNAI1)
    NM_001256414
    cg07766948 NM_024040 CUE domain containing 2 (CUEDC2)
    cg07802350 NM_000523 homeobox D13 (HOXD13)
    cg07955995 NM_138693 Kruppel like factor 14 (KLF14)
    cg19112204 NM_004171 solute carrier family 1 member 2 (SLC1A2)
    cg08097417 NM_138693 Kruppel like factor 14 (KLF14)
    cg08118942 NM_023928 acetoacetyl-CoA synthetase (AACS)
    cg08194377 NM_015245 ankyrin repeat and sterile alpha motif domain
    containing 1A (ANKS1A)
    cg08478427 NR_106988; microRNA 7641-2 (MIR7641-2)
    NM_001145522;
    NM_001145521;
    NM_001145520;
    NM_015577;
    NM_001145523;
    NM_001145525
    cg08662753 NM_001278074; collagen type V alpha 1 chain (COL5A1)
    NM_000093
    cg08856941 NM_020682 arsenite methyltransferase (AS3MT)
    cg08960065 NM_206885; solute carrier family 26 member 5 (SLC26A5)
    NM_206884;
    NM_206883;
    NR_120443;
    NR_120442;
    NR_120441;
    NM_001167962;
    NM_198999
    cg09275691 NM_020401; nucleoporin 107 (NUP107),
    NR_038930
    cg09805798 NR_110265; long intergenic non-protein coding RNA 1797
    NR_110264 (LINC01797)
    cg09965557 NM_001080779; myosin IC (MYO1C)
    NM_03375;
    NM_001080950
    cg10240079 NM_181726 ankyrin repeat domain 37 (ANKRD37)
    cg17861230 NM_000923 phosphodiesterase 4C (PDE4C)
    cg10543136 NM_018100 EF-hand domain containing 1 (EFHC1)
    cg11176990 NR_028386; uncharacterized LOC375196 (LOC375196)
    NM_001145451
    cg16867657 NM_017770 ELOVL fatty acid elongase 2 (ELOVL2)
    cg12333719 NM_006646; WAS protein family member 3 (WASF3)
    NM_001291965
    cg24724428 NM_017770 ELOVL fatty acid elongase 2 (ELOVL2)
    cg12658720 NM_203425 chromosome 17 open reading frame 82 (C17orf82)
    cg13206721 NM_020752; G protein-coupled receptor 158 (GPR158)
    NR_027333
    cg13333913 NM_012304; F-box and leucine rich repeat protein 7 (FBXL7)
    NM_001278317
    cg13460409 NM_018962 ripply transcriptional repressor 3 (RIPPLY3)
    cg13973351 NM_017966 VPS37C subunit of ESCRT-I (VPS37C)
    cg14231565 NM_001034845 polypeptide N-acetylgalactosaminyltransferase like
    6 (GALNTL6)
    cg14305139 NM_014957 DENN domain containing 3 (DENND3)
    cg19215678 NM_006312; nuclear receptor corepressor 2 (NCOR2)
    NM_001077261
    cg00097800 NM_001430 endothelial PAS domain protein 1 (EPAS1)
    cg14911690 NM_025245 PBX homeobox 4 (PBX4)
    cg15609017 NR_040046 long intergenic non-protein coding RNA 1531
    (LINC01531)
    cg15743533 NM_207121; family with sequence similarity 110 member A
    NM_001042353 (FAM110A)
    cg15761531 NM_001010983; glycosyltransferase 8 domain containing 1
    NM_152932; (GLT8D1)
    NM_018446;
    NM_152932
    cg27173374 NM_053064 G protein subunit gamma 2 (GNG2),
    transcript variant 1
    cg16267121 NM_001190472; MT-RNR2 like 3 (MTRNR2L3)
    NM_001015885;
    NM_003610
    cg16322747 NM_003440; zinc finger protein 140 (ZNF140)
    NM_001300777;
    NM_001300778;
    NM_001300776
    cg16465695 NM_014238 kinase suppressor of ras 1 (KSR1)
    cg16593468 NR_028444; protein disulfide isomerase family A member 5
    NM_006810 (PDIA5)
    cg16673857 NM_018418; spermatogenesis associated 7 (SPATA7)
    NM_001040428
    cg17343879 NM_148977; pantothenate kinase 1 (PANK1)
    NM_138316;
    NM_148978;
    NR_029524
    cg16781885 NM_001034845 polypeptide N-acetylgalactosaminyltransferase like
    6 (GALNTL6)
    cg00876345 NM_003363; ubiquitin specific peptidase 4 (USP4)
    NM_199443
    cg14756158 NM_002072 G protein subunit alpha q (GNAQ)
    cg19702785 NM_002251 potassium voltage-gated channel modifier subfamily
    member 1 (KCSN1)
    cg27394136 NM_007215 DNA polymerase gamma 2, accessory subunit
    (POLG2)
    cg18339380 NM_020225 storkhead box 2 (STOX2)
    cg18506897 NR_073547; neurexin 3 (NRXN3)
    NM_004796
    cg18768299 NM_014753 BMS1, ribosome biogenesis factor (BMS1)
    cg18815943 NM_012186 forkhead box E3 (FOXE3)
    cg10522765 NM_004544 NADH: ubiquinone oxidoreductase subunit A10
    (NDUFA10)
    cg12238343 NM_016568 relaxin family peptide receptor 3 (RXFP3)
    cg19301963 NM_032638; GATA binding protein 2 (GATA2)
    NR_125398
    cg00831672 NM_001101426; isoprenoid synthase domain containing (ISPD)
    NM_001101417
    cg19810954 NM_015833; adenosine deaminase, RNA specific B1 (ADARB1)
    NM_001160230;
    NM_001112;
    NR_027674;
    NR_027672;
    NM_015834;
    NR_027673
    cg20088545 NM_058238 Wnt family member 7B (WNT7B)
    cg20425444 NM_015310 pleckstrin and Sec7 domain containing 3 (PSD3)
    cg21165089 NM_001300803; membrane anchored junction protein (MAJIN)
    NM_001037225
    cg21962791 NM_024854 pyridine nucleotide-disulphide oxidoreductase
    domain 1 (PYROXD1)
    cg22101188 NM_001252335; cingulin like 1 (CGNL1), transcript variant 1
    NM_032866
    cg22444338 NM_001134395; chromosome 7 open reading frame 50
    NM_032350; (C7orf50)
    NM_001134396
    cg22519947 NM_024848 MORN repeat containing 1 (MORN1)
    cg22540792 NR_024191; atlastin GTPase 2 (ATL2), transcript variant 3
    NM_001308076;
    NM_001135673;
    NM_022374
    cg23128025 NM_052950 WD repeat and FYVE domain containing 2
    (WDFY2)
    cg23677767 NM_001198675; transmembrane protein 136 (TMEM136)
    NM_001198674;
    NM_001198673;
    NM_001198672;
    NM_001198671;
    NM_001198670;
    NM_174926
    cg01520297 NM_005539 inositol polyphosphate-5-phosphatase A (INPP5A)
    cg25606723 NM_015130 TBC1 domain family member 9 (TBC1D9)
    cg25642673 NM_002199 interferon regulatory factor 2 (IRF2)
    cg14681176 NM_016538 sirtuin 7 (SIRT7)
    cg26430984 NM_173465 collagen type XXIII alpha 1 chain (COL23A1)
    cg02536625 NM_003875; guanine monophosphate synthase (GMPS)
    NM_003875
    cg27320127 NM_022055 potassium two pore domain channel subfamily K
    member 12 (KCNK12)
    cg16245716 NM_021238; SIN3-HDAC complex associated factor (SINHCAF)
    NM_001135811;
    NM_001135812
    cg27540719 NM_005330 hemoglobin subunit epsilon 1 (HBE1)
    cg16950671 NM_198795 tudor domain containing 1 (TDRD1)
  • In a reduced gene set (Table 5), druggable gene targets have been selected from Table 4. In particular, the genes have been selected if an in vitro assay for determining the activity or function of the encoded protein was known in the art.
  • TABLE 5
    UCSC_RefGene_Accession Name of first accession No.
    NM_030885; microtubule associated protein 4 (MAP4)
    NM_001134364;
    NM_002375
    NM_001033582; protein kinase C zeta (PRKCZ)
    NM_002744;
    NM_001033581
    NM_001077243; glutamate ionotropic receptor AMPA type
    NM_001112812; subunit 4 (GRIA4)
    NM_001077244;
    NM_000829
    NR_046356; glutamate ionotropic receptor AMPA type
    NM_001077243; subunit 4 (GRIA4)
    NM_000829
    NM_018412; suppression of tumorigenicity 7 (ST7)
    NM_021908
    NM_006255 protein kinase C eta (PRKCH)
    NM_000720; calcium voltage-gated channel subunit
    NM_001128840; alpha1 D (CACNA1D)
    NM_001128839
    NM_004394 death associated protein (DAP)
    NM_145068 transient receptor potential cation channel
    subfamily V member 3 (TRPV3)
    NM_002569: furin, paired basic amino acid cleaving
    NM_001289823 enzyme (FURIN)
    NM_198838; acetyl-CoA carboxylase alpha (ACACA)
    NM_198837;
    NM_198839;
    NM_198836;
    NM_198834
    NM_002069; G protein subunit alpha i1 (GNAI1)
    NM_001256414
    NM_004171 solute carrier family 1 member 2 (SLC1A2)
    NM_000923 phosphodiesterase 4C (PDE4C)
    NM_017770 ELOVL fatty acid elongase 2 (ELOVL2)
    NM_017770 ELOVL fatty acid elongase 2 (ELOVL2)
    NM_006312; nuclear receptor corepressor 2 (NCOR2)
    NM_001077261
    NM_001430 endothelial PAS domain protein 1 (EPAS1)
    NM_053064 G protein subunit gamma 2 (GNG2)
    NM_148977; pantothenate kinase 1 (PANK1)
    NM_138316;
    NM_148978;
    NR_029524
    NM_003363; ubiquitin specific peptidase 4 (USP4)
    NM_199443
    NM_002072 G protein subunit alpha q (GNAQ)
    NM_002251 potassium voltage-gated channel modifier
    subfamily S member 1 (KCNS1)
    NM_007215 DNA polymerase gamma 2, accessory subunit (POLG2)
    NM_004544 NADH: ubiquinone oxidoreductase subunit A10 (NDUFA10)
    NM_016568 relaxin family peptide receptor 3 (RXFP3)
    NM_001101426; isoprenoid synthase domain containing (ISPD)
    NM_001101417
    NM_005539 inositol polyphosphate-5-phosphatase A (INPP5A)
    NM_016538 sirtuin 7 (SIRT7)
    NM_003875; guanine monophosphate synthase (GMPS)
    NM_003875
    NM_021238; SIN3-HDAC complex associated factor (SINHCAF)
    NM_001135811;
    NM_001135812
    NM_198795 tudor domain containing 1 (TDRD1)
  • Finally, a list with 68 (partially redundant) coding sequences and non-coding sequences such as miRNAs or long non-coding RNAs was selected from the 88 CpGs determined by LASSO+stepwise regression (Table 6). The table further shows the coefficients of the respective age indicator and their standard errors (see Example 5).
  • TABLE 6
    Coefficient +/−Std. Error ID UCSC_Ref_Gene
    66.2822 9.8319 cg11330075
    65.203 12.7828 cg00831672 ISPD
    55.7265 7.5377 cg27320127 KCNK12
    44.4116 8.4185 cg27173374 GNG2
    38.3902 11.4848 cg14681176 SIRT7
    37.8069 7.8695 cg06161948 GPATCH1
    36.6564 9.964 cg08224787
    31.9397 8.4487 cg05396610 GRIA4
    30.1919 9.7667 cg15609017 LINC01531
    28.089 8.4046 cg09805798 LOC101927577
    27.9392 6.4631 cg19215678 NCOR2
    27.8502 6.5183 cg12333719 WASF3
    27.226 11.4717 cg03741619 TRPV3
    27.0323 8.3075 cg16677512 ACACA
    25.9599 6.5411 cg03230469 GDNF
    25.3932 7.5404 cg19851481
    24.5374 9.2886 cg10543136 EFHC1
    22.5525 110.8777 cg07291317 MYO10
    21.8666 13.0388 cg26430984 COL23A1
    20.3621 4.083 cg16950671 TDRD1
    20.3269 4.3239 cg16867657 ELOVL2
    19.7973 11.6224 cg22077936
    18.7137 3.9634 cg08044253 GNAI1
    18.2047 6.1215 cgl2548216 MAP4
    18.1936 4.9361 cg05211227 CCDC179
    18.0812 6.0906 cg13759931
    17.6857 5.0036 cg08686931
    17.5303 4.5192 cg07955995 KLF14
    16.1143 6.2049 cg07529089 ST7
    14.8703 8.1841 cg01520297 INPP5A
    14.6684 4.3239 cg00087368 SIM1
    14.4397 9.0743 cg05087008 GRIA4
    14.4361 3.4811 cg24724428 ELOVL2
    14.3055 5.5169 cg19112204 SLC1A2
    14.2968 4.1059 cg04525002
    14.2302 9.571 cg0885694l AS3MT
    13.3831 8.8481 cg16465695 KSR1
    11.8127 8.6353 cg08097417 KLF14
    11.7798 7.2263 cg21628619
    11.3523 5.5046 cg09460489
    11.2461 3.2763 cg13460409 DSCR6
    10.6268 4.8908 cg25642673 IRF2
    10.4347 7.2693 cg19702785 KCNS1
    9.7844 7.4354 cg18506897 NRXN3
    9.5931 5.0988 cg21165089 C11orf85
    9.093 3.9039 cg27540719 HBE1
    8.9361 6.2141 cg21807065
    8.8577 3.708 cg18815943 FOXE3
    8.6138 2.8016 cg23677767 TMEM136
    7.1699 3.726 cg07802350 HOXD13
    7.0528 4.2489 cg11176990 LOC375196
    6.5416 1.9413 cg10321869
    6.5049 3.478 cg17343879 PANK1
    5.8296 2.8652 cg08662753 COL5A1
    5.696 3.7948 cg14911690 PBX4
    3.2983 1.8057 cg12804730
    3.1388 2.007 cg16322747 ZNF140
    −4.8653 3.4742 cg14231565 GALNTL6
    −5.5608 2.5813 cg10501210
    −6.047 2.4969 cg09275691 NUP107
    −6.35 3.4617 cg15008041
    −9.1942 6.2636 cg05812299 MTRNR2L5
    −9.3144 3.8416 cg24319133
    −9.4566 4.137 cg12658720 C17orf82
    −9.8704 3.0654 cg20576243
    −10.4082 3.2632 cg03473532 MKLN1
    −10.6429 7.4387 cg07381960 FURIN
    −11.1592 3.2236 cg05106770
    −12.0021 4.6698 cg04320377 KLHL42
    −12.3296 2.7158 cg19432688
    −12.9858 10.2914 cg22519947 MORN1
    −13.7116 2.9505 cg06831571
    −13.8029 3.2707 cg08194377 ANKS1A
    −13.8668 4.4903 cg01636910 BCL10
    −14.6975 11.6384 cg14305139 DENND3
    −15.0408 2.9644 cg04028695
    −16.3295 7.5252 cg15743533 FAM110A
    −16.3314 5.0278 cg03680898 PROS1
    −18.6196 4.4565 cg20088545 WNT7B
    −19.0952 3.3737 cg13333913 FBXL7
    −19.3068 7.0512 cg19301963 GATA2
    −21.5752 6.8028 cg13973351 VPS37C
    −23.0892 4.2648 cg16781885 GALNTL6
    −26.0415 6.6199 cg04287203 NRP1
    −32.3606 8.9103 cg27394136 POLG2
    −48.0918 10.9191 cg10240079 ANKRD37
    −50.0227 10.3763 cg02536625 GMPS
    −63.4434 21.7615 cg23128025 WDFY2
    • Example 7: Iterative Updating of the Age Indicator
  • The age indicator was automatically updated with cases (probands; individuals) based on the decision if the domain boundaries of the test data were outside the domain boundaries of the training set of age indicator. The domain boundaries were the minimum and maximum DNA methylation levels of each genomic DNA sequence comprised in the age indicator. The minimum and maximum DNA methylation levels were found in the original training data set which has been used for determining the age indicator. These values change any time if the values of further individuals come in and replace the original min and max values for each of the CpGs. Min values will consequently diminish (if min is not yet 0) and max values will increase (if not yet 1) per CpG. In doing so the domain boundaries of the age indicator will expand to optimal values and it will be increasingly improbable that the age indicator is further updated.
  • The updating was done with the following R code:
  •
    ##%######################################################%##
    # #
    #### Predictions with a test data set ####
    # #
    ##%######################################################%##
    prdct <− data.frame(SampleID = newsamlesdf$SampleID,
    pred_age = predict(model_blasso, newsamplesdf), stringsAsFactors = F)
    plot(newsamplesdf$Age, prdct$pred_age, pch = 16, col = “red”, xlab = “Real Age”, ylab =
    “Predicted Age”)
    abline(0,1,col = “red”)
    ##%######################################################%##
    # #
    #### If the predictions this way are ####
    #### not satisfactory need to run this ####
    # #
    ##%######################################################%##
    IME_blasso <− IME_blasso %>% dplyr:: select(Age, everything( ))
    domain <− data.frame(min=apply(as.matrix(IME_blasso[,−1]),2, min),
    max=apply(as.matrix(IME_blasso[,−1]),2, max))
    #calculate domain for new samples
    domain_curr <− data.frame(min=apply(as.matrix(newsamplesdf),2, min),
    max=apply(as.matrix(newsamplesdf),2, max))
    ##%######################################################%##
    # #
    #### operative check for prediction ####
    ##
    # ## #%######################################################%##
    if(sum((domain$min-domain_curr$min)<0 & (domain$max-domain_curr$max)>0)){
    nnew <− NROW(newsamplesdf)
    nn <− NROW(IME_blasso)
    # add new probands to the training set
    newIME_blasso <− rbind(IME_blasso, newsamplesdf) # concatenate the two set
    # rerun the model
    model_blasso_new <− step(lm(Age ~ . , data = newIME_blasso), direction = “both”)
    sstep <− summary(model_blasso_new)
    sstep
    ##check
    par(mfrow=c(1,1))
    plot(newIME_blasso$Age, model_blasso_new$fitted.values,
    xlab = “Real Age [red points = new points]”, ylab = “Predicted Age”,
    main = paste(“Stepwise Regression with IME_newModel CpGs R2 = ”,
    round(sstep$r.squared,3), sep = “”), pch = 1)
    abline(0,1,col = “red”)
    errs <− newIME_blasso$Age − model_blasso_new$fitted.values
    mae(errs)
    postResample(newIME_blasso$Age,
    as.vector(model_blasso_new$fitted.values))
    points(newIME_blasso$Age[nn:(nn+nnew)],
    as.vector(model_blasso_new$fitted.values[nn:(nn+nnew)]), col = “red”,
    pch = 16)
    ##
    predictions <− data.frame(Age = newIME_blasso$Age[nn:(nn+nnew)],
    PredAge = model_blasso_new$fitted.values[nn:(nn+nnew)])
    write.csv(predictions, “predictions.csv”)
    save(model_blasso_confy_new, file = “model_blasso_new.lm”)
    #rm(newIME_blasso)
    }else{
    predicted <− predict.lm(model_blasso_confy, newsamplesdf)
    plot(newsamplesdf$Age, predicted, pch=12, main=“Predictions with IME_model”)
    abline(coef = c(model_blasso_new,1), col = “red”)
    external_pred <− data.frame(PredAge= predicted, RAge = newsamplesdf$Age)
    postResample(predicted, newsamplesdf$Age)
    }
    • Example 8: Further Statistical Analyses of Data and Prediction of Age
  • DNA has been sampled from app. 200 individuals. These samples have all been obtained in northern Germany, but in order to have a broad database, care was taken to not exclude any individual in view of factors such as chronological age, general health state, obesity, level of physical fitness, drug consumption including drugs such as nicotine and alcohol. Therefore, the group is considered to be representative for the general population.
  • CpG methylation levels of the DNA from biological samples of app. 100 individuals have been determined using the method of Example 1, resulting in a large number of app. 850.000 (850000) CpGs for each individual.
  • In view of the amount of data and the computational expense of its analysis, the data was split into smaller arbitrary groups, and then, the data of these smaller groups was analyzed.
  • Using the data of a first group of 16 individuals, a principal component analysis has been effected and it was found that about 10 principal components account for almost all of the variance observed in the methylation levels of the CpGs in the groups samples, with the first two components already covering 98% of the variation, clearly indicating that despite the extremely large number of different CpG methylation levels considered, a reduction of the number is advised. Based on the principal component analysis and using regression techniques, a predictor model was established for each group that however basically showed that the model constructed was still suffering from insignificance of some of the coefficients.
  • It was also determined that even so, a number of the coefficients determined were found to have no statistical significance.
  • Given this, data from a first larger group of 98 individuals was analysed with the intention of establishing a model having a clearly reduced number of CpGs to be considered while maintaining a high statistical significance of all parameters. To this end, first a LASSO regression was executed; note that LASSO regression is a technique well known in the art and that software packages to implement Lasso regression are readily available. Note that it is possible to distinguish whether or not the methylation levels of a given CpG are of particular statistical relevance or not; this allows to consider only CpGs having some relevance. In particular, in this respect, reference is being made to “The biglasso Package: A Memory- and Computation-Effic Solver for LASSO Model Fitting with Big Data in R” by Yaohui Zeng and Patrick Breheny in arXiv:1701.05936v2 [statCO] 11 Mar. 2018. Using a selection of only 50 different CpGs determined to constitute an optimal set by the LASSO regression, an attempt was made to further optimize the model derived. This was done using the XgBoost algorithm. Note that XgBoost is a well known open-source software library which provides a gradient boosting framework for a number of languages. Note that XgBoost serves to amend coefficients used in a statistical model. For further details with respect to the XgBoost algorithm and the implementation thereof, reference is made to “XGBoost: A Scalable Tree Boosting System”, by T. Chen and C. Guestrin, arXiv: 1603.02754v3, 10. Juni 2016. The contents of the cited documents is enclosed herein in its entirety for purposes of disclosure.
  • It was found that a performant model could be obtained yielding good regression coefficients.
  • However, rather than contenting oneself with having achieved a high regression coefficient for the group considered, and maintaining the performant model as is, data from another 98 individuals were analyzed in the same manner as before. It was found that for the second group, about 78 CpGs should be considered in a model, with 8 of the 78 CpGs overlapping with the 50 CpGs selected for the first arbitrary group of 98 individuals.
  • Then, another run was made and it was determined that in a merged group, 70 CpG would constitute a useful selection of CpG from the initially considered app. 850000 different CpGs. From these 70 CpG, 10 were overlapping with only those of the first group, 12 were were overlapping with only those of the second group and 8 were overlapping with both groups.
  • The regression performed with XgBoost allowed to maintain the same high performance after 20 rounds of cross-validation.
  • This shows that by statistical means, in particular a LASSO regression, PCA or other means of distinguishing whether or not a specific CpG of a large number of CpG has statistical relevance, the number of CpGs can be significantly reduced from an overall extremely large set to a rather small set, allowing cheap detection using methods as referred to in Examples 2 and 3 above.
  • Then, relating only to the small set of CpGs, a useful model can be established that despite the small number of CpGs considered allows a determination of an age with high precision and a small confidence intervall, in particular by re-iterating parameters of a statistical model established.
  • In this manner, despite an overall small number of CpGs considered, determination of an age will be quite precise initially and will have a reliability increasing with time.

Claims (52)

1. A method for determining an age indicator comprising the steps of
(a) providing a training data set of a plurality of individuals comprising for each individual
(i) the DNA methylation levels of a set of genomic DNA sequences and
(ii) the chronological age, and
(b) applying on the training data set a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), thereby determining the age indicator and a reduced training data set,
wherein the independent variables are the methylation levels of the genomic DNA sequences and wherein the dependent variable is the age,
wherein the age indicator comprises
(i) a subset of the set of genomic DNA sequences as ensemble and
(ii) at least one coefficient per genomic DNA sequence contained in the ensemble, and wherein the reduced training data set comprises all data of the training data set except the DNA methylation levels of the genomic DNA sequences which are eliminated by the LASSO.
2. A method for determining the age of an individual comprising the steps of
(a) providing a training data set of a plurality of individuals comprising for each individual
(i) the DNA methylation levels of a set of genomic DNA sequences and
(ii) the chronological age, and
(b) applying on the training data set a regression method comprising a Least Absolute Shrinkage and Selection Operator (LASSO), thereby determining the age indicator and a reduced training data set,
wherein the independent variables are the methylation levels of the genomic DNA sequences and wherein the dependent variable is the age,
wherein the age indicator comprises
(i) a subset of the set of genomic DNA sequences as ensemble and
(ii) at least one coefficient per genomic DNA sequence contained in the ensemble, and wherein the reduced training data set comprises all data of the training data set except the DNA methylation levels of the genomic DNA sequences which are eliminated by the LASSO, and
(c) providing the DNA methylation levels of the individual for whom the age is to be determined of at least 80% or 100% of the genomic DNA sequences comprised in the age indicator, and
(d) determining the age of the individual based on its DNA methylation levels and the age indicator,
wherein the determined age can be different from the chronological age of the individual.
3. The method of claim 1, wherein the regression method further comprises applying a stepwise regression subsequently to the LASSO.
4. The method of claim 3, wherein the stepwise regression is applied on the reduced training data set.
5. The method of claim 1, wherein the ensemble comprised in the age indicator is smaller than the set of genomic DNA sequences.
6. The method of claim 1, wherein the ensemble comprised in the age indicator is smaller than the set of genomic DNA sequences comprised in the reduced training data set.
7. The method of 3, wherein the stepwise regression is a bidirectional elimination, wherein statistically insignificant independent variables, are removed, wherein the significance level is 0.05.
8. The method of claim 1, wherein the LASSO is performed with the biglasso R package or by applying the command “cv.biglasso” or wherein the “nfold” is 20.
9. The method of claim 1, wherein the regression method does not comprise a Ridge regression (L2 regularization) or the L2 regularization parameter/lambda parameter is 0.
10. The method of claim 1, wherein the LASSO L1 regularization parameter/alpha parameter is 1.
11. The method of claim 1, wherein the age indicator is iteratively updated comprising adding the data of at least one further individual to the training data in each iteration, thereby iteratively expanding the training data set.
12. The method of claim 11, wherein in one updating round the added data of each further individual comprise the individual's DNA methylation levels of
(i) at least 5% or 50% or 100% of the set of genomic DNA sequences comprised in the initial or any of the expanded training data sets, and/or
(ii) the genomic DNA sequences contained in the reduced training data set.
13. The method of claim 11, wherein all genomic DNA sequences (independent variables) which are not present for all individuals who contribute data to the expanded training data set are removed from the expanded training data set.
14. The method of claim 11, wherein in one updating round the set of genomic DNA sequences whereof the methylation levels are added is identical for each of the further individual(s).
15. The method of claim 11, wherein one updating round comprises applying the LASSO on the expanded training data set, thereby determining an updated age indicator and/or an updated reduced training data set.
16. The method of claim 11, wherein the training data set to which the data of the at least one further individual are added is the reduced training data set, which can be the initial or any of the updated reduced training data sets.
17. The method of claim 16, wherein the reduced training data set is the previous reduced training data set in the iteration.
18. The method of claim 11, wherein one updating round comprises applying the stepwise regression on the reduced training data set thereby determining an updated age indicator.
19. The method of claim 1, wherein in one updating round, the data of at least one individual is removed from the training data set and/or the reduced training data set.
20. The method of claim 11, wherein the addition and/or removal of the data of an individual depends on at least one characteristic of the individual, wherein the characteristic is the ethnos, the sex, the chronological age, the domicile, the birth place, at least one disease and/or at least one life style factor, wherein the life style factor is selected from drug consumption, exposure to an environmental pollutant, shift work or stress.
21. The method of claim 1, wherein the quality of the age indicator is determined, wherein the determination of said quality comprises the steps of
(a) providing a test data set of a plurality of individuals who have not contributed data to the training data set comprising for each said individual
(i) the DNA methylation levels of the set of genomic DNA sequences comprised in the age indicator and
(ii) the chronological age; and
(b) determining the quality of the age indicator by statistical evaluation and/or evaluation of the domain boundaries,
wherein the statistical evaluation comprises
(i) determining the age of the individuals comprised in the test data set,
(ii) correlating the determined age and the chronological age of said individual(s) and determining at least one statistical parameter describing this correlation, and
(iii) judging if the statistical parameter(s) indicate(s) an acceptable quality of the age indicator or not or wherein the statistical parameter is selected from a coefficient of determination (R2) and a mean absolute error (MAE), wherein a R2 of greater than 0.50 or greater than 0.70 or greater than 0.90 or greater than 0.98 and/or a MAE of less than 6 years or less than 4 years or at most 1 year, indicates an acceptable quality, and
wherein evaluation of the domain boundaries comprises
(iv) determining the domain boundaries of the age indicator,
wherein the domain boundaries are the minimum and maximum DNA methylation levels of each genomic DNA sequence comprised in the age indicator and wherein said minimum and maximum DNA methylation levels are found in the training data set which has been used for determining the age indicator, and
(v) determining if the test data set exceeds the domain boundaries, wherein not exceeding the domain boundaries indicates an acceptable quality.
22. The method of claim 1, wherein the training data set and/or the test data set comprises at least 10 or at least 30 individuals or at least 200 individuals or wherein the training data set comprises at least 200 individuals and the test data set at least 30 individuals.
23. The method of claim 21, wherein the age indicator is updated when its quality is not acceptable.
24. The method of any of claim 11, wherein the age of the individual is determined based on its DNA methylation levels and the updated age indicator.
25. The method of claim 2, wherein the age of the individual is only determined with the age indicator when he/she has not contributed data to the training data set which is used for generating said age indicator.
26. The method of any of claim 1, wherein the age indicator is not further updated when the number of individuals comprised in the data has reached a predetermined value and/or a predetermined time has elapsed since a previous update.
27. The method of claim 1, wherein the set of genomic DNA sequences comprised in the training data set is preselected from genomic DNA sequences whereof the methylation level is associable with chronological age.
28. The method of claim 27, wherein, the preselected set comprises at least 400000 or at least 800000 genomic DNA sequences.
29. The method of claim 1, wherein the genomic DNA sequences comprised in the training data set are not overlapping with each other and/or only occur once per allele.
30. The method of claim 1, wherein the reduced training data set comprises at least 90 or at least 100 or at least 140 genomic DNA sequences.
31. The method of claim 1, wherein the reduced training data set comprises less than 5000 or less than 2000 or less than 500 or less than 350 or less than 300 genomic DNA sequences.
32. The method of any of claim 1, wherein the age indicator comprises at least 30 or at least 50 or at least 60 or at least 80 genomic DNA sequences.
33. The method of any of claim 1, wherein the age indicator comprises less than 300 or less than 150 or less than 110 or less than 100 or less than 90 genomic DNA sequences.
34. The method of claim 1, wherein the DNA methylation levels of the genomic DNA sequences of an individual are measured in a sample of biological material of said individual comprising said genomic DNA sequences.
35. The method of claim 34, wherein the sample comprises buccal cells.
36. The method of claim 34, further comprising a step of obtaining the sample, wherein the sample is obtained non-invasively.
37. The method of claim 34, wherein the DNA methylation levels are measured by methylation sequencing, bisulfate sequencing, a PCR method, high resolution melting analysis (HRM), methylation-sensitive single-nucleotide primer extension (MS-SnuPE), methylation-sensitive single-strand conformation analysis, methyl-sensitive cut counting (MSCC), base-specific cleavage/MALDI-TOF, combined bisulfate restriction analysis (COBRA), methylated DNA immunoprecipitation (MeDIP), micro array-based methods, bead array-based methods, pyrosequencing and/or direct sequencing without bisulfate treatment (nanopore technology).
38. The method of claim 34, wherein the DNA methylation levels of genomic DNA sequences of an individual are measured by base-specific cleavage/MALDI-TOF and/or a PCR method or wherein base-specific cleavage/MALDI-TOF is the Agena technology and the PCR method is methylation specific PCR.
39. The method of claim 34, wherein the DNA methylation levels of the genomic DNA sequences comprised in the age indicator are determined in a sample of biological material comprising said genomic DNA sequences of the individual for whom the age is to be determined.
40-72. (canceled)
73. A data carrier comprising the age indicator obtained by the method of claim 2.
74. (canceled)
75. The method of claim 1, wherein the training data set, reduced training data set and/or added data further comprise at least one factor relating to a life-style or risk pattern associable with the individual(s).
76. The method of claim 75, wherein the factor is selected from drug consumption, environmental pollutants, shift work and stress.
77. The method of 75, wherein the training data set and/or the reduced training data set is restricted to sequences whereof the DNA methylation level and/or the activity/level of an encoded proteins is associated with at least one of the life-style factors.
78. The method of claim 75, further comprising a step of determining at least one life-style factor which is associated with the difference between the determined and the chronological age of said individual.
79. A method of determination of an age indicator for an individual in a series of individuals, the determination being based on levels of methylation of genomic DNA sequences found in the individual,
wherein
based on methylation levels of an ensemble of genomic DNA sequences selected from a set of genomic DNA sequences having levels of methylation associable with an age of the individuals
an age indicator for the individual is provided
in a manner relying on a statistical evaluation of levels of methylation for genomic DNA sequences of the plurality of individuals,
wherein
the age indicator for the individual is provided
in a manner relying on a statistical evaluation of levels of methylation for genomic DNA sequences of a plurality of individuals which is different from the plurality of individuals that was referred to for a preceding statistical evaluation used for the determination of the same age indicator of an individual preceding in the series,
the difference of the pluralities of individuals being caused in that a plurality of individuals used for the first statistical evaluation is amended at least by inclusion of at least one additional preceding individual from the series,
and wherein
the age indicator for the individual is provided in a manner where the at least two different statistical evaluations of the two different plurality of individuals result in a change of at least one coefficient used when calculating the age indicator from the methylation levels of an ensemble and/or result in levels of methylation of different genomic DNA sequences or CgP loci found being considered.
80. The method of age determination of an individual according to claim 79, based on the levels of methylation of genomic DNA sequences found in the individual,
comprising
providing a set of genomic DNA sequences from genomic DNA sequences having levels of methylation associable with an age of the individual;
determining for a plurality of individuals levels of methylation for the genomic DNA sequences of the set;
selecting from the set an ensemble of genomic DNA sequences
such that
the number of genomic DNA sequences in the ensemble is smaller than or equal to the number of genomic DNA sequences in the set,
and
ages of the individuals can be calculated based on the levels of methylation of the sequences of the ensemble;
determining in a sample of biological material from the individual the levels of the methylation of at least the sequences of the ensemble;
calculating an age of the individual based on levels of the methylation of the sequences of the ensemble;
judging whether or not
a re-selection of genomic DNA sequences of the ensemble is necessary and/or the way an age of the individual based on levels of the methylation is calculated is to be altered, or in view of a statistical assessment,
depending on the judgment,
amending the group of individuals to include the individual;
and at least one of
re-selecting an ensemble of genomic DNA sequences from the set based on determinations of the levels of the methylation of individuals of the amended group
and/or
changing of at least one coefficient used when calculating the age indicator from the methylation levels of an ensemble.
81. The method of age determination of an individual according to claim 80, comprising the steps of
preselecting
from genomic DNA sequences having levels of methylation associable with an age of the individual the set of genomic DNA sequences;
determining for a plurality of individuals levels of methylation for the preselected genomic DNA sequences;
selecting from the preselected set an ensemble of genomic DNA sequences
such that
the number of genomic DNA sequences in the ensemble is smaller than the number of genomic DNA sequences in the preselected set,
ages of the individuals can be calculated based on the levels of methylation of the sequences of the ensemble,
and
a statistical evaluation of the ages calculated indicates an acceptable quality of the calculated ages;
determining in a sample of biological material from the individual levels of the methylation of the sequences of the ensemble;
calculating an age of the individual based on levels of the methylation of the sequences of the ensemble;
calculating a statistical measure of the quality of the age calculated;
judging whether or not the quality according to the statistical measure is acceptable or not;
outputting the age of the individual calculated if the quality is judged to be acceptable;
determining that a re-selection of genomic DNA sequences is necessary if the quality is judged to be not acceptable,
amending the group of individuals to include the individual;
re-selecting an ensemble of genomic DNA sequences from the preselected subset based on determinations of the levels of the methylation of individuals of the amended group.
82-91. (canceled)
92. A chip comprising a number of spots or less than 500 or less than 385 or less than 193 or less than 160 spots, adapted for use in determining methylation levels, the spots comprising at least one spot or several spots specifically adapted to be used in the determination of methylation levels of at least one of cg11330075, cg25845463, cg22519947, cg21807065, cg09001642, cg18815943, cg06335143, cg01636910, cg10501210, cg03324695, cg19432688, cg22540792, cg11176990, cg00097800, cg09805798, cg03526652, cg09460489, cg18737844, cg07802350, cg10522765, cg12548216, cg00876345, cg15761531, cg05990274, cg05972734, cg03680898, cg16593468, cg19301963, cg12732998, cg02536625, cg24088134, cg24319133, cg03388189, cg05106770, cg08686931, cg25606723, cg07782620, cg16781885, cg14231565, cg18339380, cg25642673, cg10240079, cg19851481, cg17665505, cg13333913, cg07291317, cg12238343, cg08478427, cg07625177, cg03230469, cg13154327, cg16456442, cg26430984, cg16867657, cg24724428, cg08194377, cg10543136, cg12650870, cg00087368, cg17760405, cg21628619, cg01820962, cg16999154, cg22444338, cg00831672, cg08044253, cg08960065, cg07529089, cg11607603, cg08097417, cg07955995, cg03473532, cg06186727, cg04733826, cg20425444, cg07513002, cg14305139, cg13759931, cg14756158, cg08662753, cg13206721, cg04287203, cg18768299, cg05812299, cg04028695, cg07120630, cg17343879, cg07766948, cg08856941, cg16950671, cg01520297, cg27540719, cg24954665, cg05211227, cg06831571, cg19112204, cg12804730, cg08224787, cg13973351, cg21165089, cg05087008, cg05396610, cg23677767, cg21962791, cg04320377, cg16245716, cg21460868, cg09275691, cg19215678, cg08118942, cg16322747, cg12333719, cg23128025, cg27173374, cg02032962, cg18506897, cg05292016, cg16673857, cg04875128, cg22101188, cg07381960, cg06279276, cg22077936, cg08457029, cg20576243, cg09965557, cg03741619, cg04525002, cg15008041, cg16465695, cg16677512, cg12658720, cg27394136, cg14681176, cg07494888, cg14911690, cg06161948, cg15609017, cg10321869, cg15743533, cg19702785, cg16267121, cg13460409, cg19810954, cg06945504, cg06153788, and cg20088545.
93. A chip according to claim 92, wherein the spots comprise at least 10 spots for CpG loci or 20 spots for CpG loci or at least 50 spots for CpG loci or spots for all of the CpG loci listed in the claim 92.
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